The recent development of fecal-genetic capture-mark-recapture (CMR) methods has increased the feasibility of estimating abundance of forest-dwelling ungulates that are difficult to survey using visual methods. Unless genetic markers differentiating sex are incorporated into such studies, however, genetic CMR approaches risk missing sex-specific differences in population trends. We developed a singlereaction genetic assay for sex and individual identification, including 10 microsatellites and an SRY marker, and applied it in the context of a post-fawning CMR study of Columbian black-tailed deer (Odocoileus hemionus columbianus) in forested habitat of coastal California during 2011 and 2012. We measured sexspecific abundance and sex ratios in high-quality summer habitats encompassing 4 distinct fawning areas. We detected a significant interaction between sex and year, indicating different trends in the abundance of males and females. We also detected a significant decline in abundance of females between years (P ¼ 0.045), which agreed with independent telemetry-based estimates, and significant differences in female abundance among fawning areas (P ¼ 0.020) but no significant differences in the abundance of males for either variable (F 1-3,20 < 0.710, P > 0.410). When sex was not considered in the analysis, we found no significant differences in abundance between the 2 years, suggesting that differing trends between the 2 sexes obscured the femalespecific patterns. We estimated average local (i.e., on the high-quality summer ranges) density (D) for females at 41.0 (AE 5.9) deer/km 2 in 2011 and 29.1 (AE 6.8) deer/km 2 in 2012, and local density of males at 15.7 (AE 3.0) deer/km 2 across the 2 study years. Accordingly, sex ratios differed between years (95% CI ¼ 3.0-4.2 F:M ratio in 2011, 2.0-2.3 F:M ratio in 2012). Incorporating sex and individual markers into a single assay provided a cost-effective means of applying CMR estimation based on fecal DNA to a high-density ungulate population in a forested ecosystem and emphasized the importance of explicitly modeling sex in abundance estimation. Ó