Chinook salmon (Oncorhynchus tshawytscha) transplanted from the Sacramento River, California, U.S.A., to New Zealand in the 1900s colonized many South Island rivers, which now show significant population-specific phenotypic variation. To characterize this variation, we conducted a morphometric analysis of two New Zealand populations and the fall-run Battle Creek population at the Coleman Hatchery, the apparent ancestral stock. Variation in length at age, weight at length, fin lengths, hump depth, snout length, and caudal peduncle width was detected among populations. Sexually mature Battle Creek and New Zealand chinook salmon were consistently identifiable from morphometric data (97.7% classification accuracy), largely through differences in caudal peduncle width and hump depth. The two New Zealand spawning populations, although distinguishable in morphology in 1994 (mean of 80% correct classification), did not classify as well using the same discriminant functions in 1995 (mean of 62.7% correct), suggesting interannual multivariate effects. Little variation was observed between the two mainstem river populations in adults collected shortly after entering freshwater. Although the genetic or environmental causes for the differences between populations have yet to be determined, our results provide empirical evidence of phenotypic divergence over decadal time scales. This work may be relevant to considerations in the development and monitoring of salmon recovery and conservation programs.