We compared marking success for larval and juvenile fishes immersed in alizarin red S (ARS) to that of fish immersed in alizarin complexone (AC). Postlarval and juvenile central stonerollersCampostoma anomalumand southern redbelly dacePhoxinus erythrogasterand larval white suckersCatostomus commersoniwere immersed in ARS or AC at concentrations of 50–400 mg/L for 6–24 h. Both chemicals imparted a violet-red mark, visible in the whole otoliths under a bright-field light source. Immersion in ARS at 200–300 mg/L for 12 or 24 h resulted in optimal marking success (100%) and minimal mortalities (0–3%). Marking success and mortalities were similar for ARS and AC in comparable treatments. Alizarin red S marks were retained for at least 160 d.