Genetic data suggest that the littoral and pelagic forms of brook charr Salvelinus fontinalis in Lake Bondi are two populations with partial reproductive isolation and non-random mating. Genetic differentiation between the two groups was supported by differences in allele frequencies and by deviation from Hardy-Weinberg equilibrium when the two groups were pooled; no such deviation was observed when fish were divided into littoral and pelagic groups. In contrast to Lake Bondi, no clear evidence of genetic differentiation was observed in Lake Ledoux. Discriminant function analyses of morphological characters support the existence of littoral and pelagic groups in Bondi and Ledoux Lakes. In Lake Bondi, the two groups differed significantly in two shape variables (pelagic fish had shorter dorsal fins, and longer body length posterior to the dorsal fin than littoral ones) whereas in Lake Ledoux, the groups differed in four shape variables (pelagic fish had shorter pectoral fins, shorter dorsal fins, and a shorter and higher caudal peduncle than littoral ones). Discriminant analyses of these characters were effective in reclassifying fish into their appropriate groups in both populations, with an efficiency of 78% for juveniles in Lake Bondi and 69% for adults in Lake Ledoux. Differences in morphology between the two forms are consistent with adaptations required to forage in each zone, i.e. benthic form in the littoral zone and planktivorous form in the pelagic zone.