Non-invasive genetic sampling (NGS) methods have been instrumental in providing robust population abundance and density estimates of bears. We conducted a small pilot study to (1) evaluate 2 NGS methods of hair traps and bear rubs in the Russian Far East (RFE) on sympatric populations of Asiatic black bears (Ursus thibetanus) and brown bears (Ursus arctos), and (2) to identify potential DNA marker sets for future study. Genetic analysis required 6 microsatellite markers to definitively identify individuals plus a gender marker, and closed population models estimated 142 Asiatic black bears and 18 brown bears. Spatially-explicit mark–recapture (SECR) density estimates for brown bears were 3 bears/100 km². Inflated Asiatic black bear estimates resulted from a lack of recaptures, although using combined detection data from the 2 NGS methods was found to improve precision for abundance estimates. Capture probabilities were higher for brown bears than for Asiatic black bears, but overall recapture probabilities were low for both species. The frequency of rubbing declined from June to August, possibly due to bears leaving the study area, and Asiatic black bears were detected less frequently on rubs than brown bears, suggesting that species-specific ecology must be incorporated into future study designs. We recommend that future applications of NGS in the RFE improve capture probabilities by sampling earlier in the season to mitigate geographic closure violation for abundance estimates and to increase the number of detections for robust spatially explicit capture–recapture analyses. Our results demonstrate that NGS methods have strong potential for monitoring of bear populations in the RFE.