Levels of differentiation in morphological traits (age at maturity, body length at age, egg mass and body depth) and spawning time were examined in sockeye salmon Oncorhynchus nerka from three geographically proximate but physically distinct creeks in Lake Aleknagik, Alaska. Happy Creek fish had significantly greater values for most measured morphological traits, and Eagle Creek fish spawned significantly later than fish in the other creeks. Phenotypic differentiation between creeks, measured as PST, was then compared with microsatellite marker differentiation between creeks, measured as FST. No correlations were apparent between PST and FST values, and PST values were generally significantly larger than zero (PST= 0·0018–0·31) whereas FST values were not (FST=−0·0004 to 0·0016). The insignificant pair-wise FST values between creek samples indicated that gene flow occurs between creeks, assuming the creek populations have reached migration–drift equilibrium. However, the strong homing behaviour of sockeye salmon precludes a scenario in which fish from the three creeks constitute a single population that segregates by body size. Rather, significant phenotypic differentiation suggests that strong divergent selection occurs on the phenotypic traits despite the homogenizing effects of gene flow.