Growth polymorphisms occur in many fish species, particularly in northern temperate freshwater lakes. The only known growth polymorphism in walleye (Sander vitreus) is in Lake Winnipeg, Canada, where slow-growing (dwarf) and fast-growing (normal) morphotypes co-exist. We examined differences in reproductive traits between forms to determine whether divergence in growth rates was accompanied by divergence in reproductive strategies and also assessed the genetic composition of both forms using mitochondrial and microsatellite DNA to determine their origin and potential reproductive isolation. Both sexes of the dwarf form produced relatively larger gonads than the normal form. Female dwarfs also had a lower liver lipid concentration, a higher ovary lipid concentration, and produced relatively larger eggs compared to the normal form. There was also some indication that dwarf and normal females differed in the fatty acid profiles of their egg lipids. Population genetic analysis based on partial sequencing of the mitochondrial control region and genotyping nine microsatellite loci indicated a single interbreeding population and sympatric origin for both morphotypes. The dwarf form appears to make a relatively larger reproductive investment at a given body size, and the differences between the two forms may result from plastic developmental responses to subtle differences in niche use.