Amplification by the polymerase chain reaction and sequencing of a highly variable segment (199 base pairs) of mitochondrial DNA (mtDNA) in 491 fish from 22 streams and 9 hatcheries revealed 9 mtDNA types in steelhead trout (Oncorhynchus mykiss), 5 types in coho salmon (O. kisutch), and 6 types in chinook salmon (O. tshawytscha). Likelihood chi-square analysis of frequencies of mtDNA types in eight paired comparisons of hatchery and geographically proximate wild populations of Oncorhynchus showed significant differences in mtDNA genotypes. More mtDNA types were found, on average, in contemporary hatchery populations for each species than in geographically proximate wild stocks. Factors potentially leading to genetic differences in hatchery and wild stocks sampled in California were historic introductions of geographically divergent populations into hatchery brood stocks and lack of introgression of geographically divergent genotypes from the hatchery into wild populations.
