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It is advantageous for fish to choose different substrate types and brightness based on their current life cycle stage, foraging requirements, predator avoidance and water conditions. We determined the substrate type and brightness preference of hatchery‐reared and wild juvenile Schizothorax wangchiachii and Percocypris pingi under laboratory conditions. Individuals and groups were exposed to four kinds of substrate types (sand: diameter < 1 mm, small gravel: diameter approximately 2–3 cm, large gravel: diameter approximately 10–15 cm, sand and medium gravel mix: diameter approximately 4–7 cm) and two kinds of substrate brightness (black and white). The results showed that hatchery‐reared and wild S. wangchiachii and P. pingi significantly preferred large gravel and black substrates regardless of the number of fish (p <.05). P. pingi had a significantly higher preference for black substrate than S. wangchiachii both in hatchery‐reared and wild individuals (p <.05). Hatchery‐reared and wild individuals of the two species shared a preference for large gravel and black substrates suggesting that substrate preferences might be genetically based. The findings in the present study could be used to improve the rearing conditions for the two species in hatchery and thereafter to enhance its adaptability after releasing to the wild. [ABSTRACT FROM AUTHOR]