Feral horses (Equus caballus) in the Garfield Flat Herd Management Area in western Nevada exist as 2 subpopulations most of the year and as a single population once sufficient snow has accumulated to free them from dependence on their respective water sources. Populations were examined for genetic structure using 12 equine microsatellite markers. Microsatellite data also were generated from a distant population in the Granite Range Herd Management Area, in northwestern Nevada. Analyses of microsatellite allele frequencies supported the genetic individuality of the 3 groups. The Garfield Hills groups were marginally differentiated by virtue of low F_ST and low success in population assignment. Recent population bottlenecks and behavioral isolation are the likely mechanisms for the genetic differences between the 2 Garfield groups. Both Garfield groups were strongly differentiated from the Granite Range horses. Allele frequencies of both Garfield Flat subpopulations were within Hardy-Weinberg expectations, whereas the Granite Range frequencies were not, suggesting population structure beyond that previously identified.