Abstract– Allozyme and mitochondrial DNA (mtDNA) data were obtained from pink salmon throughout Prince William Sound, Alaska, from two hatchery, five upstream, and 20 tidal locations distributed among five management regions collected during 1994. Screening for allozymes included 66 loci for 92 to 100 fish per sample. Thirty-four loci had variant allele frequencies <0.01 in one or more collections and were used for population analyses. Eight haplotypes were detected after screening 40 fish per collection for variation at the ND5/ND6 region of mtDNA using six restriction enzymes. Significant and apparently stable differences detected by both data sets permit rejecting a null hypothesis of panmixia and support managing native populations in Prince William Sound at the regional level. Distinctions between upstream and tidal collections were detected within Lagoon Creek (allozymes) and Koppen Creek (mtDNA). Significant regional heterogeneity was detected within upstream (allozymes and mtDNA) and tidal (allozymes) collections; however, upstream collections were more divergent from each other than were tidal collections. The absence of distinction of Armin F. Koernig Hatchery from almost all regions was consistent with multiple origins of this stock. Conversely, Solomon Gulch Hatchery in the East Region was distinct from all regions but East, consistent with a more restricted origin and influence.