Genetic variation was studied at two polymorphic loci for ∼3 yr (November 1978–February 1982) in juvenile sand flounder (Rhombosolea plebeia) in Wellington Harbour, New Zealand. The Gpi-1 locus showed a heterogeneity in genotype frequencies, but this was not clearly related to season or to fish length. At the Gpi-2 locus, genotype frequencies were dependent upon length and showed a significant excess of homozygotes in juveniles but not in adults. This latter phenomenon has been reported previously in several species of marine molluscs, and so may be common to marine organisms producing large numbers of pelagic larvae. Reasons for the excess of homozygotes are discussed, and it is suggested that assortative mating is the most likely explanation and that this is an area of marine population genetic research which has been over-looked.