AbstractDistinguishing hatchery‐reared fishes from wild conspecifics can be required to quantify the success of augmentation programmes. This study estimated the probability of identifying calcein‐marked, hatchery‐reared Colorado pikeminnow Ptychocheilus lucius Girard from external and internal structures. Both control and marked fish held in the laboratory were correctly identified 80% of the time after 300 days. A fluorometer was more accurate 180 days post‐marking, whereas visual observation was more discriminating at 300 days. There were no differences in detection rates among structures in laboratory fish, and for most structures of fish held outdoors, detection rates were <20%. Overall, a strong negative effect of light on mark persistence was observed. Also, an initial positive effect of fish size on mark fluorescence and a negative effect of fish growth were detected. These results suggest the potential use of calcein as a batch‐marking tool would be aided by future studies that better quantify light exposure and calcein mark persistence in both field and experimental settings.