The flagship species for San Diego County's vernal pools is the federally endangered San Diego fairy 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.