Brown bears (Ursus arctos) inhabit much of the northern hemisphere, including portions of North America, Europe, and Asia. Whereas northern populations generally are healthy, their distribution becomes fragmented and conservation status more tenuous in their southern range. Many fragmented populations across southern Asia are poorly understood, and abundance and distribution data are minimal. One such population contains the Gobi bear, a brown bear surviving in the Great Gobi Strictly Protected Area of southwestern Mongolia. The number of bears in this area was assumed to be low, without data-based abundance estimates. Whereas bears frequent 3 oases complexes, it was not known to what extent bears moved or bred among these complexes, which span approximately 300 km. As part of a larger science-based conservation effort, we conducted a DNA-based mark–recapture population survey in 2009 to estimate abundance, inter-oases movements of individual bears and geneflow, and genetic variability. We placed barb-wire hair-collection sites surrounding 13 supplemental feeders at most water sources within the 3 oases complexes: Atas–Inges, Shar Khuls, and Tsagaan Bogd. During 5 sessions throughout spring and summer, we collected 600 bear hair samples and genotyped 205 samples at 12 variable microsatellite loci (from 24). We identified 21 individual bears (14 M and 7 F) 48 times and developed a mark–recapture population estimate of 22 bears (95% CI = 21–29). Estimates of mean detection probability were 0.27 (SE = 0.09, CI = 0.13–0.49) and 0.51 (SE = 0.063, CI = 0.39–0.64) for female and male bears, respectively. One female and 4 males were sampled at 2 oases complexes and 3 males were sampled at all 3 oases complexes. The genetic variability (heterozygosity) was low compared with other brown bear populations. We suggest this population is isolated from other bear populations and is likely critically endangered with fewer than 40 individuals.