One of the challenges of ecology and conservation is to understand how habitat features influence species movement patterns. Landscape genetics provides a promising framework for investigating the interaction between landscape parameters and gene flow. This can be especially important for species that have undergone population declines due to habitat loss and fragmentation. We investigated the effects of different landscape features on gene flow between populations of the northern Idaho ground squirrel (Spermophilus brunneus brunneus; NIDGS), an endangered subspecies, and the southern subspecies (S. b. endemicus; SIDGS), a candidate for ESA listing. We sampled 448 individuals from 14 NIDGS populations and 502 individuals from 12 SIDGS populations. Genotypes were generated for 8 microsatellite loci and data were analyzed with STRUCTURE, BAPS, SAMOVA, non-metric multidimensional scaling, and PathMatrix. Preliminary results indicated that each subspecies contains isolated populations and each can be broadly divided into two genetic groups. For the NIDGS, one group included 8 colonies in the eastern portion of the study area and the second group included 6 colonies in the west. There was limited gene flow between groups, with increased movement from west-to-east. Neither of the genetic differences between groups were highly correlated with landscape features such as elevation, vegetation types, rivers or slope. The SIDGS also were divided into 2 groups, with 3 colonies in the north that were divided by the Weiser River from 9 colonies in the southern part of the study area. Only limited gene flow was detected across the Weiser River suggesting that this landscape feature was an effective barrier to movement. Our results suggest greater connectivity among populations than indicated by previous field-base studies, which has implications for conservation and management of this endemic species.