It’s important to understand species-habitat relationships over time for effective adaptive management of rare species. We report results from 10-years of track tube monitoring of the two largest extant populations of the federally endangered Pacific pocket mouse (PPM) on Marine Corps Base Camp Pendleton (MCBCP). Total area occupied by PPM has ranged from 117 to 335 ha, with a recent estimate of 165 ha. Dynamic occupancy and structural equation modeling have shown PPM spatial and temporal dynamics are positively associated with open ground, forb and perennial herb cover, while negatively associated with non-native grass cover (NNG), which is strongly influenced by rainfall and fire. MCBCP have used these results to support fire and vegetation management resulting in largely positive PPM responses and colonization of new areas. Due to regulatory concerns about habitat maintainence in PPM occupied areas, management actions have been largely limited to sparsely occupied or unoccupied habitats or after major population declines. Inclusion of habitat maintenance in PPM occupied areas may promote resiliency and reduce population stochasticity, chances of population decline and loss of genetic diversity. We discuss concurrent research on phenology, climate, and diet; and show the power of this program in supporting a monitoring-management feedback loop.