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Schizothorax wangchiachii is a key fish species in the stock enhancement program of the Yalong River hydropower project, China. Alizarin red S (ARS) was used to mark large numbers of juvenile S. wangchiachii in the Jinping Hatchery and later used to evaluate stock enhancement in the Jinping area of the Yalong River. In a small-scale pilot study, 7,000 juveniles of the 2014 cohort were successfully marked by immersion in ARS solution, and no mortality was recorded during the marking process. The ARS mark in the fish otoliths remained visible 20 months later. In the large-scale marking study, approximately 600,000 juveniles of the 2015 cohort were successfully marked. Mortalities of both marked and unmarked juveniles were very low and did not differ significantly. Total length, wet mass and condition factor did not differ significantly between unmarked and marked individuals after three months. On 24 July 2015, about 840,000 Jinping Hatchery-produced young S. wangchiachii, including 400,000 marked individuals, were released at two sites in the Jinping area. Recapture surveys showed that (1) marked and unmarked S. wangchiachii did not differ significantly in total length, wet mass and condition factor; (2) stocked individuals became an important part of recruitment of the 2015 cohort; (3) instantaneous growth rate of marked individuals tended to slightly increase; and (4) most stocked individuals were distributed along a 10–15 km stretch near the release sites. These results suggest that the ARS method is a cost-efficient way to mass mark juvenile S. wangchiachii and that releasing juveniles is an effective means of stock recruitment.