Mark-recapture studies for investigating migration patterns and population dynamics of large numbers of individuals require an effective, non-lethal marking technique. Our goal in the present study was to determine the suitability of visible implant elastomer (VIE) for a species in nominal decline, Etheostoma moorei (Yellowcheek Darter). Mortality and mark retention were initially studied in a laboratory setting using a surrogate species, Etheostoma caeruleum (Rainbow Darter) due to Yellowcheek Darter's conservation status (candidate species for listing as endangered). There was 100% survival and mark retention over the 58-day period for the fourteen Rainbow Darters injected with VIE marks, and there were no observable lesions or scars resulting from marking. Adult Yellowcheek Darters ≥30 mm (n = 385) were individually marked with VIE, and their soft dorsal fins were clipped. They were then returned to their original riffle sites on the Middle and South forks of the Little Red River, AR. There were a total of 26 recapture events, with a mark retention rate of 88% (12% of recaptures had evidence of fin clips, yet no VIE marks). The interval between initial capture and last recapture ranged from 13–401 days. We identified no relationship between position of injection, color marked, or darter size at injection and mark retention. The duration of the present study (13 months) appears suitable for VIE mark retention in Yellowcheek Darter. Adults are both slow-growing and short-lived, characteristics which enhance the suitability of VIE for mark-recapture use.