Visible implant elastomer (VIE) and injectable photonic dye (IPD), two types of injectable fluorescent marks, have shown promise in previous applications in a variety of fishes but have not been extensively tested on darters. We marked a species from each of two genera of darters, Percina and Etheostoma, in a laboratory experiment to determine the influence of VIE and IPD marks on survival and the influences of mark type, location, and color on mark retention. Short‐term (≤80‐d) survival was similar between marked and control specimens for both marks in both species. Over the long term (200–240 d), however, the survival rate for IPD‐marked Roanoke darters P. roanoka was significantly lower than that for controls (50% versus 80%), whereas VIE‐marked Roanoke darters had a survival rate (88%) similar to that of controls. Long‐term survival of riverweed darters E. podostemone did not differ among groups. In Roanoke darters, the mark retention rate for IPD was significantly lower than that for VIE by day 80 of the experiment (80% versus 94%), and ventral IPD marks were retained with greater frequency than were dorsal IPD marks. In riverweed darters, retention was similar for VIE and IPD (79% versus 83%) in all body locations through day 240. In both species, yellow IPD marks exhibited higher retention rates than did green IPD marks, whereas the reverse was true for yellow and green VIE marks. Overall, VIE was a superior mark in the Percina representative but performed similarly to IPD in Etheostoma. Because of interspecific and intraspecific variability in mark performance, we recommend a pilot study before initiating field use of injectable marks in untested species.