Vertebral numbers in hatchery-reared and wild populations of masu salmon Oncorhynchus masou were compared. In addition, vertebral numbers were analyzed in wild masu salmon juveniles from rivers in which hatcheryreared fry, juveniles, and smolts had been stocked. Hatchery-reared masu salmon had fewer vertebrae than fish from wild populations. This difference may have been caused by environmental factors (incubation water temperatures) during the early developmental stages. Wild masu salmon from a river in which stock enhancement programs have been continued for a long time had fewer vertebrae than wild fish from neighboring rivers. Stock enhancement programs may genetically affect the vertebral number in wild masu salmon populations.