We examined Chinook salmonOncorhynchus tshawytschapopulations in the Yukon Territory for variation in age and size of spawning adults, juvenile morphology, and biochemical genetics during 1985–1987. Yukon River Chinook salmon spent at least one winter in fresh water as juveniles; about 6% of the returning adults had spent two winters in fresh water as juveniles. Males matured at younger ages and generally at smaller mean lengths at age than did females. We observed differences in juvenile morphology among populations: juveniles in habitats with faster water velocities had larger fins and thicker bodies than those in habitats with slower water velocity. We also observed genetic differentiation among populations; the greatest difference was between those populations in the Yukon River drainage and an Alsek River population. Within the Yukon River drainage, Chinook salmon from the Whitehorse fishway and Takhini River were distinct from other populations surveyed. We noted some variation in allelic frequencies between adults and juveniles sampled from the same location and found annual stability of allelic frequencies for the 16 variable loci examined.