Normal and dwarf size forms of lake whitefish (Coregonus clupeaformis) from Como Lake, Ontario, were sampled at spawning time and examined for differences in electrophoretic, mtDNA, and morphological characteristics to test the hypothesis of reproductive isolation and provide clues regarding evolutionary origin. Of the 36 enzyme loci examined, 33 were fixed for the same alleles in both dwarf and normal lake whitefish. At the three polymorphic loci, allele frequencies were not statistically different between dwarfs and normals. mtDNA analysis revealed five different haplotypes. The same mtDNA haplotype was the most common in both dwarf and normal lake whitefish, but there was a statistically significant difference in haplotype frequencies between the two size forms. Discriminant and principal component analyses demonstrated highly significant morphological differences between dwarfs and normals. Because the two size morphs spawn in the same place at the same time, it is most likely that genetic differences, not different rearing environments, underly the observed morphological differences. mtDNA haplotypes derived from both the Mississippi and Atlantic glacial refugia are present in Como Lake lake whitefish, raising the possibility of an allopatric divergence for the two forms; however, this hypothesis requires testing by genetic comparisons of other sympatric populations in Ontario.