A relict population of unique desert dwelling brown bears (Ursus arctos) inhabits a series of remote oases along the southern portion of the Great Gobi Strictly Protected Area in Mongolia. Little is known about these bears, which may number as few as 25 animals. We used noninvasive genetic techniques in an attempt to estimate minimum population size, determine sex ratios, and evaluate genetic diversity and degree of isolation between population centers. Between 1996 and 1998 we collected 200 hair samples using hair-traps from rub posts and attempted to amplify 6 microsatellite loci for 75 samples with 3 or more follicles. Microsatellite amplification rates were low (63%), and 3 loci were monomorphic. Complete genotypes could be obtained for only 28 samples, which provided a minimum count of 8 bears. Observed heterozygosity (0.29) and average number of alleles (2) were very low compared to other brown bear populations. Genetic data were obtained for only 2 of the 3 population centers, and sample sizes were not large enough to accurately evaluate sex ratio or levels of isolation. A 263 base-pair segment of the mitochondrial DNA control region was sequenced for 3 bears and a single control region haplotype was obtained. This haplotype was identical to a previously published haplotype for the Gobi bear, and earlier work has shown that this haplotype is closely related to brown bear haplotypes from Pakistan. Future genetic analyses that attempt to use hair or fecal samples will need to increase the number of loci to provide sufficient resolving power for individual identification and should attempt to collect fresher samples to increase success rates. The detection of very low levels of genetic diversity supports the hypothesis that this population is very small and isolated from other brown bear populations. Further studies of the Gobi bear and conservative management actions are greatly needed.