Feral horses roaming North America are distinct not only because of their acclimatization to the wild but also because of their diversified ancestry. The wild horses inhabiting the Ochoco National Forest near Prineville, Oregon, are one of the remaining wild mustang herds and are protected by the Wild Horse and Burro Acts of 1971 and 1978. With deterioration of their rangeland, drought, vegetation conditions, human encroachment, fencing off of grazing lands, competition with wildlife, and other livestock grazing on public lands, a critical balance between conserving the natural ecology of rangelands and protecting and managing the wild horses needs to be monitored. Supplementing traditional visual censuses with genetic analyses can enhance management and conservation efforts because DNA analyses provide insight into the genetic fitness and inbreeding status of the population. The objective of this study was to provide a genetic analysis using noninvasive sample collection methods to assess the genetic health of this small herd and to determine their genetic fitness. A total of 52 individuals from the Big Summit wild horse herd and adjacent herd management areas (HMAs) were genotyped for 17 short tandem repeat (STR) loci, mtDNA haplogroups, and major histocompatibility complex STR loci. Cluster analysis exhibited an admixed population with discernable contribution from Iberian ancestry, the major influence coming from Andalusian and Lusitano breeds. The deficiency of hetero zygosity, a deviation from Hardy–Weinberg equilibrium, together with a positive inbreeding coefficient for the neutral STRs in the Big Summit population suggested a parallel to an “island population” phenomenon leading to loss of genetic diversity within the herd. These findings improve understanding of the genetic structure of feral herds from different HMAs, which in turn will enable enhanced conservation and management strategies.