Sterlet (Acipenser ruthenus), one of the last sturgeons in the Danube basin, is regularly stocked in national and international restoration programs, but the efficacy of stocking has not yet been evaluated. Effectiveness of stocking should involve marking and evaluating growth and survival of juveniles. Chemical marking with alizarin red S (ARS) was evaluated to establish optimal ARS staining approaches for juvenile sterlet. Bathing in a 100–200 mg l−1 ARS concentration for 12 h had no affect on fish mortality or growth. Use of a green laser on the upper five external structures (dorsal, lateral, and ventral scutes and rostral and anal plates) allowed easy detection for at least a year. Simultaneous use of multiple external structures was effective for distinguishing stocked from wild fish without harm or sacrifice. We conclude that ARS staining enabled a cost‐effective, quick, and labour‐nonintensive way to mark sterlet, with a high‐field detectability and minimal previous experience required.