Phenotypic change in closely related lineages frequently follows a common pathway in response to similar environmental conditions. This process, termed parallel evolution, results in the evolution of similar but independently derived ecotypes. Individuals with a blue phenotype are observed in some populations of walleye (Sander vitreus) from Laurentian Shield lakes. The blue phenotype may represent a case of parallel evolution: previous morphological studies revealed significant differences compared with the yellow phenotype as well as numerous lake-specific characteristics among blue individuals. The genetic variability of blue and yellow walleye phenotypes from 6 Laurentian Shield lakes was estimated using AFLP. Results clearly indicate that, whatever their phenotype, individuals from a given lake were more similar genetically than those from other lakes. However, blue and yellow phenotypes represent different populations within each lake. These results suggest the colonization of each lake by a single group of walleye followed by the parallel origin of the blue phenotype. The parallel evolution of the blue walleye phenotype could represent an excellent model for studying mechanisms underlying divergent selection and reproductive isolation.