The overall purpose of this study was to evaluate the methodology of the 2010 burrowing owl survey protocol. The specific purpose of the analysis presented here is to use data collected according to the burrowing owl monitoring protocol to estimate occupancy for both burrowing owls and California ground squirrels within the sample frame. The expected detection probability for owls was much lower than anticipated. In general, efforts should be made in future studies to increase detection probability for both owls and squirrels. Possible ways to improve detection include (a) better training of field personnel, (b) more consistent application of the monitoring protocols, (c) changes in the protocol such as the number of visits per site or the time spent at a site during each visit, and (d) improved field equipment and consistent used of the same equipment. If this work is to be repeated in the future, the monitoring protocol should more clearly describe the method for collecting ground squirrel data. Habitat covariates associated with suitable burrowing owl habitat were not able to be identified. In the future, conceptual models need to be developed to guide data collection and analysis, with attention to the spatial and temporal scale of the covariates related to habitat suitability.