The salt marsh harvest mouse (Reithrodontomys raviventris) is a federal and California listed endangered mammal endemic to the San Francisco Bay. The objectives of this research were to determine habitat use of endangered salt marsh harvest mice in a managed marsh in Fremont California, and to evaluate whether managed flooding of the marsh provides favorable habitat conditions for the mice. In addition, this research explores the effectiveness of using mark-recapture model selection analysis to estimate capture probability, survival, and population growth rate for salt marsh harvest mice. Mice were captured for four nights per month between May and August, 2008. Thirty-six unique salt marsh harvest mice were captured for a catch per 100 nights of trap effort of 1.9. The sex ratio of male to female mice was skewed towards males with a sex of 2.3:1. Salt marsh harvest mice were distributed randomly throughout the marsh and no relationships were found between mice distribution and pickleweed salinity, pickleweed height, distance to levees, distance to dry or filled water bodies, percent cover of vegetation, or sympatric rodents. The findings of this study indicate that catch-per-trap-effort, the current standard method to estimate salt marsh harvest mice populations, may not be accurate. The results of this study can be used by managers of salt marsh harvest mice habitat to manage and estimate mouse populations
