The salt marsh harvest mouse (SMHM, Reithrodontomys raviventris) is a federally listed endangered species endemic to the coastal marshes of the San Francisco Bay Estuary. We combined range wide field survey data and conservation genomics to help identify population segments of particular concern. We resolved genetic units corresponding to the known subspecies. However, we also identified a previously unrecognized discrete genetic lineage near Richmond. Our survey of the species found that the population at Richmond is the last one remaining throughout all the central portion of the SMHM range. The populations in the central Bay were likely the first ones founded when the San Francisco Bay was reformed after the Pleistocene. Thus, these central populations are ancestral to those in the species strongholds in the south San Francisco Bay and to the north in San Pablo and Suisun Bays. Our analyses also indicated that the Richmond population had extremely low genetic diversity. The population is isolated on a small patch of habitat surrounded by urban features with minimal high tide escape habitat. It is in severe jeopardy of being wiped out by sea level rise, additional anthropogenic changes in the adjacent urban area, or through stochastic events.