The domestication of ayu Plecoglossus altivelis, in which breeding has been carried out for multiple generations without the introduction of exotic broodstock (purebred-styled cultivation), causes rapid loss of genetic variability, and is problematic for resource management programs. The introduction of wild paternity to enhance genetic variability was examined for its effects on the performance of the newly hybridized stock using the Gunma population (hatchery strain), which has been inbred for 29 generations since its origin. Principal component analysis showed that hybridization could modify the stock performance, moderately affecting behavior and morphometrics. Reinforcement of aggressiveness as well as transformation to a long-nosed shape in the hybrid population contributed revised performance that was acceptable to sports fishers as an artificial stock. To reduce genetic stress for native ayu populations, the introduction of wild paternity is proposed through sperm from wild caught specimens to hybridize with eggs from the pure-bred hatchery population.