Parallel (or convergent) evolution provides strong evidence for a deterministic role of natural selection: similar phenotypes evolve when independent populations colonize similar environments. In reality, however, independent populations in similar environments always show some differences: some nonparallel evolution is present. It is therefore important to explicitly quantify the parallel and nonparallel aspects of trait variation, and to investigate the ecological and genetic explanations for each. We performed such an analysis for threespine stickleback (Gasterosteus aculeatus) populations inhabiting lake and stream habitats in six independent watersheds. Morphological traits differed in the degree to which lake–stream divergence was parallel across watersheds. Some aspects of this variation were correlated with ecological variables related to diet, presumably reflecting the strength and specifics of divergent selection. Furthermore, a genetic scan revealed some markers that diverged between lakes and streams in many of the watersheds and some that diverged in only a few watersheds. Moreover, some of the lake–stream divergence in genetic markers was associated within some of the lake–stream divergence in morphological traits. Our results suggest that parallel evolution, and deviations from it, are primarily the result of natural selection, which corresponds in only some respects to the dichotomous habitat classifications frequently used in such studies.