In the stickleback family (Gasterosteidae), divergence in pelvic morphology is typically associated with reproductive isolation and ecological niche specialization. In this study, we assessed whether reproductive isolation may be involved in the persistence of within-lake polymorphism in brook stickleback (Culaea inconstans (Kirtland, 1840)). We studied populations of brook stickleback in central Alberta, Canada, that are polymorphic for pelvic reduction (i.e., presence–absence of pelvic spines). We investigated the persistence of the pelvic polymorphisms over 40 generations in five lakes. We found that, of the five populations examined, the frequencies of pelvic phenotypes have remained unchanged in three populations, the polymorphism has persisted with significantly changed frequencies of pelvic phenotypes in one population, and the polymorphism has been lost in one population. Using 10 microsatellite loci, we observed low genetic divergence between individuals with and without pelvic spines in one lake, suggesting a lack of assortative mating among individuals with divergent pelvic phenotypes. This observation suggests that the pelvic polymorphism in brook stickleback persists due to balancing selection in the absence of reproductive isolation, although the selective forces were not evaluated. The significant changes in phenotypic frequencies in two populations are likely associated with environmental disturbances such as species introductions.