Basic Information
Common Name: San Diego Fairy Shrimp
Scientific Name: Branchinecta sandiegonensis
Species Code: BRASAN
Management Category: SL (species at risk of loss)
Occurrence Map
Table of Occurrences

Species Information

MSP Species Background

Goals and Objectives

Goal: Protect, enhance, and restore San Diego fairy shrimp occupied and historically occupied habitat to create resilient, self-sustaining populations that provide for persistence over the long-term (>100 years).

local NFO 2018, 2019, 2020, 2021 SL

Management units: 2, 3, 4, 5, 6

Beginning in 2018, conduct annual qualitative surveys during the wet season to determine the presence of San Diego fairy shrimp in vernal pools on Conserved Lands. Every 3 years conduct dry season quantitative cyst soil sampling at a rotating panel of vernal pools to determine the density of San Diego fairy shrimp cysts, as identified by genetic analysis. Use methods and protocols specified in the City of San Diego Vernal Pool Management and Monitoring Plan (VPMMP; 2015) . Determine whether the pools fall into Level 1 (stable), Level 2 (enhancement) or Level 3 (restoration) management categories based on the presence of shrimp among pools in each complex and track increases or declines in cyst densities over 3 monitoring years to determine if movement is triggered between management categories as identified in the VPMMP. If there is sufficient decline in San Diego fairy shrimp cyst density to trigger an increase in management levels as identified in the VPMMP, then more intensive monitoring is required to determine topographic or hydrologic disturbances as described in the VPMMP.

Action Statement Action status Projects
IMP-1 Submit project metadata, datasets, and monitoring reports with management and Monitoring recommendations to the MSP Web Portal. Available for implementation
Criteria Deadline year
Annual Qualitative Surveys Conducted for San Diego Fairy Shrimp and Quantitative Cyst Sampling Every 3 Years with Reports Completed 2021
Threat Name Threat Code
Altered hydrologyALTHYD
Human uses of the PreservesHUMUSE
Invasive plantsINVPLA
Connectivity Strategic Plan for Western San Diego County Science Session
A strategic plan for connectivity (CSP) of preserve lands in western San Diego County was developed for the San Diego Association of Government's Environmental Mitigation Program Working Group (EMPWG) in 2011. It was prepared by the SDMMP utilizing the input from a science workshop held in 2010. Many of the high priority items in the CSP have been completed and the data collected over those several years were utilized to inform management decisions. In 2014, there was a need to update and refocus the connectivity strategies and priorities for implementation. The purpose of this meeting was to gather input for the updated CSP. It followed a similar format to the 2010 connectivity workshop. The meeting consisted of a review of completed and in process projects, followed by breakout groups, and then an integration of ideas and recap session. The breakout groups were: (1) Large Animals and Landscape Connectivity; (2) Small Animals; and (3) Pollinators. The meeting focused on: 1. Identifying species to focus questions on connectivity; 2. Identifying questions and objectives to be considered for connectivity for species, and 3. Identifying available methodologies for addressing the questions and objectives. The updated CSP is found in Volume 3 of the Management Strategic Plan.
Human impact to vernal pool complexes in Southern California
The flagship species for San Diego County’s vernal pools is the federally endangered San Diegofairy shrimp (Branchinecta sandiegonensis: SDFS). For this species, the most critical management issues are likely to involve population connectivity. Degradation of the landscape, direct damage (often by vehicles), creation of new basins (most often “road ruts”), and increasing biotic connectivity (beyond historic levels) are also important factors.The specific goals of this study were focused in three areas: landscape genetics in the San Diego fairy shrimp B. sandiegonensis; hybridization between B. sandiegonensis and B. lindahli; and conservation, management and recovery of B. sandiegonensis. This was a project jointly funded by SANDAG and a CDFW Section 6 grant.
J26 Vernal Pool Monitoring- Vista Del Mar Elementary School Project
Five-year monitoring of vernal pool reference site J26 Vernal Pool Complex as part of the comprehensive mitigation program associated with the construction of the San Ysidro School District's Vista Del Mar Elementary School. The J26 Complex is formally recognized by the USFWS as a vernal pool reference site. It is located 10 km north of the restoration area. Vernal pools in the J26 Complex were chosen as control pools to monitor restoration success. This includes monitoring of San Diego fairy shrimp populations, vernal pool plant germination and abundance, and levels of inundation in a healthy vernal pool system.
Proctor Valley Vernal Pools and Uplands Habitat Restoration Project
The Proctor Valley Vernal Pool and Uplands Habitat Restoration Project will complete restoration of 19 acres of vernal pools and coastal sage scrub in Proctor Valley on the City of San Diego's Otay Lakes Cornerstone Lands, a biological core area under the San Diego MSCP. The Project includes restoration of vernal pools and coastal sage scrub habitat and establishment of occurrences of two high-priority Management Strategic Plan (MSP) plants with seed collection, seed bulking, propagation, planting and seeding, and maintenance. The Project also includes restoration of habitat specific to the needs of several MSP animal species through seeding and planting of host and nest plants, construction of artificial burrows, and other measures. Project partially funded by SANDAG TransNet EMP Land Management Grant #5001972 and #5004955.
Vernal Pool Restoration
The vernal pools at the Spring Canyon/Goat Mesa complex (J16-J18) and surrounding open space have suffered considerable off-road damage over the years. This damage has resulted in changes in hydrologic, flow patterns, and inundation characteristics. This vernal pools complex was identified by the adopted Recovery Plan for Vernal Pools of Southern California (USFWS 1998) as necessary to stabilize populations of the following endangered and threatened MSP species: E. aristulatum, P. nudiuscula, N. fossalis, O. californica, B. sandiegonensis, and S. wootoni. The Management Strategic Plan (MSP) for Conserved Lands in Western San Diego County (SDMMP) also lists other MSP species historically found onsite, including D. variegata, M. minimus, S. hammondii, and A cunicularia. Minimization of illegal off-road vehicle use is the primary goal. The main objective to reach the goal is to use to fence off as many of the key access points and areas of frequent off-road vehicle use throughout the City open space to protect the habitat for the endangered and threatened species that exist onsite. This will be done by hiring a fence contractor to provide all supplies and install the fence.
File name Lead Author Year Type
2009 Progress Report for the Shinohara Vernal Pool Complex Weed Control Project Olson, Meagan 2009 report
2010-11 Baseline Survey Report for the Jamul Mountains Parcels of the the Otay Ranch Preserve O'Meara, Cailin; Sundberg, J.R.; Dodero, Mark 2011 report
Annual Report for the Otay Ranch Preserve January 1 - December 31, 2012 O'Meara, Cailin; Bennett, Anna; Dodero, Mark 2013 report
Appendix D. Year 5 VDM Fairy Shrimp Survey 2016 report
Appendix E. CRAM report Year 5 2016 report
Biannual Report for Otay Ranch Preserve January 1-April 30, 2013 O'Meara, Cailin; Bennett, Anna; Dodero, Mark 2013 report
City of San Diego Vernal Pool And Quino Habitat Restoration Project Implementation Report 2010 report
Connectivity Project Summary: San Diego Fairy Shrimp Bohonak, Andrew; Simovich, M 2014 powerpoint presentation
Connectivity Strategic Plan for Western San Diego County Science Session - July 1, 2014 Connectivity Project Summaries Bohonak, Andrew; Boydston, Erin; Brehme, Cheryl; Brown, Chris; Clark, Denise; Fisher, Robert N.; Hung, Keng-Lou James; Jennings, Megan; Lewison, Rebecca; Lyren, Lisa; Mitelberg, Anna; Rochester, Carlton; Simovich, M; Tracey, Jeff; Vickers, Winston 2014 workshop summary
County of San Diego MSCP Monitoring Summary Report January 1998 - June 2007 County of San Diego 2007 report
Final Report: Human impact to vernal pool complexes in Southern California Bohonak, Andrew; Simovich, M 2014 report
Final Report: Vernal Pool Habitat Restoration at Otay Mesa Open Space 2020 report
Management Plan for "S" Series Vernal Pools on San Diego National Wildlife Refuge Martin, John 2006 report
MSCP vernal pool inventory City of San Diego (USFWS) Conservation genetics of the endangered fairy shrimp species Branchinecta sandiegonensis Bohonak, Andrew 2005 report
Restoration of the S-series Vernal Pools on the Shinohara Parcel of San Diego National Wildlife Refuge Martin, John; Terp, Jill 2014 report
Revised Final City of San Diego Vernal Pool Habitat Conservation Plan Management and Monitoring Plan 2020 report
Shinohara Vernal Pool Presence/Absence Survey for Fairy Shrimp 2009 report
Vernal Pool Management MCB Camp Pendleton Raitter, William 2023 powerpoint presentation
Vernal Pool and Quino Habitat Restoration and Management Recommendations Report 2007 report
Vernal Pool And Quino Habitat Restoration Project Implementation Report 2010 report
Vernal Pool Management and Monitoring 2019 Berninger, Mark 2019 powerpoint presentation
Vernal Pool Restoration Final Report 2018 report
Weed Control on the Vernal Pool Restoration Areas of the San Diego National Wildlife Refuge: Jamul, California 2013 report
Year 1 Vista Del Mar Report 2013 report
Year 2 Vista Del Mar Annual Report 2013 report
Year 3 Vista Del Mar Fairy Shrimp Report 2014 report
Year 4 Vista Del Mar Fairy Shrimp Report 2015 report
Year 4 Vista Del Mar Report 2015 report
Year 5 Vista Del Mar Report 2016 report

Current Distribution Rangewide

Endemic to southern California and restricted to vernal pools and other non-vegetated temporary (i.e., containing water a short time) basins in coastal southern California and northwestern Baja California, Mexico [1].

Known Populations in San Diego County

Within MSPA, San Diego fairy shrimp are known from vernal pools and vernal pools complexes in MU1 (Tijuana Slough NWR, Imperial Beach), MU2 (Kearny Mesa, Chollas Heights), MU3 (Sweetwater Reservoir, Marron Valley, Otay Mesa), MU4 (Mission trails Regional Park, Santee, Poway), MU5 (Ramona), MU6 (Del Mar Mesa, Lopez Ridge, Mira Mesa, Carlsbad, San Marcos) [2]. Also known from vernal pools on MCAS Miramar which supports the largest contiguous block of habitat and highest number of occupied vernal pools within the range of the San Diego fairy shrimp (39 complexes; over 1,899 pools) [1].

List Status

FE [3].

Habitat Affinities

Vernal pool habitat specialists, found in small, shallow vernal pools 5-30 cm (2-12 in) deep with a temperature range of 10-20°C (50-68°F) [3]. They are occasionally found in ditches and road ruts that support suitable conditions [1].

Taxonomy and Genetics

A small freshwater crustacean in the family Branchinectidae, of the Order Anostraca [4]. Described by Michael Fugate in 1993 based on specimens collected on Del Mar Mesa, San Diego County, California [5]. Closely related to Branchinecta lynchi (vernal pool fairy shrimp), a narrow California endemic and a federally threatened species [3,6]. The San Diego fairy shrimp is often misidentified with the versatile fairy shrimp (Branchinecta lindahli), which is native to and commonly found throughout western North America [4]. Genetic studies have found that populations of San Diego fairy shrimp are defined by pool complexes rather than by individual vernal pools which are considered subpopulations [7].

Seasonal Activity

Usually observed from January-March or later in years with early or late rainfall, when seasonal rainfall fills vernal pools [1].

Life History/Reproduction

Has large stalked compound eyes and no carapace (shell covering the back) [8]. They swim upside down using 11 pairs of swimming legs. Mature males can reach 9-16 mm (0.4-0.6 inch) in length, and mature females range in length from 8- 14 mm (0.4-0.5 inch) [4]. Can be distinguished from other Branchinecta fairy shrimp by the shape of the second antenna in the males, or the shape and length of the ventral ovisac in females. They are also distinguished by a of pair of dorsilateral spines [4, 5].San Diego fairy shrimp cysts hatch and mature within 7 to 14 days of rainfall filling a pool, depending on water temperature [9]. Cysts either drop to the pool bottom or remain in the brood sac until the female dies and sinks [1]. Fairy shrimp disappear after about one month [8].


Fairy shrimp disappear after about one month [8]. Only a fraction of the cysts may hatch when pools refill in the same rainy season creating a cyst “bank” in soils with several years of breeding [8, 10]. This partial hatching of cysts helps the San Diego fairy shrimp persist in its seasonal and variable environment [11]. Cysts are capable of withstanding temperature extremes and prolonged drying, but are vulnerable to crushing [8, 12].


Threatened by habitat loss and degradation due to filling, grading, discing, and leveling, urban and agricultural development, road projects, grazing, off-road vehicle use, trampling, invasion from weedy nonnative plants, trash dumping, soil compaction, erosion, drought, habitat fragmentation and isolation of vernal pool systems and complexes, and alteration of the watershed [3,4]. Destruction of watersheds and disruption of hydrological systems can create further impacts by creating barriers to dispersal, such that reproductive output may be inhibited [13]. The loss and modification of vernal pool habitat continues to be a significant threat to the San Diego fairy shrimp, especially in areas where urbanization is expected to expand [1,13]. Vehicles may negatively affect fairy shrimp by disrupting pool hydrology and chemistry, crushing cysts, displacing adults or cysts to unsuitable locations, or creating conditions favorable for invasion of nonnative plants that degrade pool habitat [12].

Special Considerations:

The ability to develop and maintain cyst banks is vital to the long-term survival of San Diego fairy shrimp populations [14, 15]. Surveys may miss observing and collecting adults, because not all vernal pools fill in a given year, pools may not fill long enough for dormant cysts to hatch, and in any given pool that has ponded water long enough to hatch San Diego fairy shrimp cysts, only a small percentage of the cyst bank hatches (i.e., bet-hedging) [16, 11]. Water chemistry and temperature are important factors in San Diego fairy shrimp populations presence and persistence [10]. San Diego fairy shrimp play an important role in the vernal pool ecosystems they inhabit as they are a food source for waterfowl, other invertebrates, and the sensitive spadefoot toad [4]. Most San Diego fairy shrimp populations are found in San Diego County [11].

Literature Sources

[1] U.S. Fish and Wildlife Service. 2008. Brancinecta sandiegonensis San Diego Fairy Shrimp 5-Year Review: Summary and Evaluation. Carlsbad, CA.

[2] MSP-MOM. 2014. Management Strategic Plan Master Occurrence Matrix. San Diego, CA. Available:

[3] U.S. Fish and Wildlife Service. 1997. Determination of Endangered Status for the San Diego Fairy Shrimp. Federal Register 62, No. 22: 4925–4939.

[4] U.S. Fish and Wildlife Service. 1998. Vernal Pools of Southern California Recovery Plan. Portland, OR.

[5] Fugate, M. 1993. Branchinecta sandiegonensis, a new species of fairy shrimp (Crustacea: Anostraca) from western North America. Proceedings of the Biological Society of Washington 106: 296-304.

[6] Simovich, M. A. and M. Fugate 1992. Branchiopod diversity in San Diego County, California. Transactions of the Western section of the Wild/We Society 28: 6-14.

[7] Bohonak, A.J. 2005. Conservation genetics of the endangered fairy shrimp species Branchinecta sandiegonensis. MSCP Vernal Pool Inventory, City of San Diego, CA.

[8] Eriksen, C. and D. Belk. 1999. Fairy Shrimps of California's Puddles, Pools, and Playas. Mad River Press, Inc., Eureka, California.

[9] Hathaway, S.A. and M.A. Simovich, 1996. Factors affecting the distribution and co-occurrence of two southern Californian anostracans (Branchiopoda), Branchinecta sandiegonensis and Streptocephalus woottoni. Journal of Crustacean Biology 16(4): 669-677.

[10] Gonzalez, R.J., J. Drazen, S. Hathaway, B. Bauer, and M. Simovich. 1996. Physiological correlates of water chemistry requirements in fairy shrimps (Anostraca) from southern California. Journal of Crustacean Biology 16: 315-322.

[11] Simovich, M.A. and S.A. Hathaway. 1997. Diversified bet-hedging as a reproductive strategy of some ephemeral pool anostracans. Journal of Crustacean Biology 17: 38-44.

[12] Hathaway, S.A., D.P. Sheehan, and M.A. Simovich. 1996. Vulnerability of branchiopod cysts to crushing. Journal of Crustacean Biology 16(3): 448-452.

[13] Bauder, E.T. 1987. Threats to San Diego Vernal Pools and Case Study in Altered Pool Hydrology. ed. T.S. Elias, 209-213, Conservation and Management of Rare and Endangered Plants. Proceedings from a conference of the California Native Plant Society.

[14] Ripley, B.J., J.H. Holtz, and M.A. Simovich. 2004. Cyst bank life-history model for a fairy shrimp from ephemeral ponds. Freshwater Biology 49: 221-231.

[15] Simovich, M.A. 2005. Considerations for the Management of Vernal Pool Faunal Communities. U.S. Department of Agriculture, Forest Service General Technical Report PSW-GTR-195.

[16] Philippi, T.E., M.A. Simovich, E.T. Bauder, and J.A. Moorad. 2001. Habitat ephemerality and hatching fractions of a diapausing anostracan (Crustacea: Branchiopoda). Israel Journal of Zoology 47: 387-395.