: Estimating population size in a mark‐recapture framework using DNA obtained from remotely collected genetic samples (e.g., feces) has become common in recent years but rarely has been used for ungulates. Using DNA extracted from fecal pellets, we estimated the size of an argali (Ovis ammon) population that was believed to be isolated from others within the Big Pamir Mountains, Afghanistan, an area where access was difficult and expensive. We used closed‐capture models to estimate abundance, and Pradel models to examine closure assumptions, both as implemented in Program MARK. We also made visual counts of argali in the Big Pamirs, allowing comparison of count indices of abundance with modeled estimates. Our model‐averaged estimate for female argali in the Big Pamir was 172 (95% CI = 117–232), which was about 23% higher than our best assessment using uncorrected visual counts. However, mark‐recapture models suggested that males were not a closed population; thus, we were unable to provide a meaningful estimate of overall population size. Males either suffered much higher mortality than females during the sampling period, or, more likely, males moved in and out of the Big Pamir area. Although information from DNA did not provide a clear overall population estimate, it suggested that the Big Pamir was not isolated from other argali populations, which could not have been confirmed with visual observations alone. Estimating argali population size using mark‐recapture models and fecal DNA is feasible but may be too expensive for frequent monitoring of large and remote populations. Our study demonstrates the importance of sex identification and separate abundance estimation for each sex, especially if movement ecology differs by sex.

We quantified population connectivity and genetic variation in the Marco Polo subspecies of argali mountain sheep (Ovis ammon polii) by genotyping 9 neutral and 8 candidate gene microsatellite loci in 172 individuals noninvasively sampled across five study areas in Afghanistan, China, and Tajikistan. Heterozygosity and allelic richness were generally high (mean H = 0.67, mean A = 6.1), but were significantly lower in the China study area (H = 0.61, P \ 0.001; A = 4.9, P \ 0.01). One marker in an immune system gene (TCRG4) showed an excess of rare alleles compared to neutral expectations. Another immune system gene (GLYCAM-1) showed excessive differentiation (high F ST ) between study areas. Estimates of genetic differentiation were similar (F ST = 0.035 vs. 0.033) with and without the two loci deviating from neutrality, suggesting that selection is not a primary driver of overall molecular variation, and that candidate gene loci can be used for connectivity monitoring, as long as selection tests are conducted to avoid biased gene flow estimates. Adequate protection of argali and maintenance of inter-population connectivity will require monitoring and international cooperation because argali exhibit high gene flow across international borders.