The relationships between glucose-6-phosphate isomerase (Gpi) genotype and quantitative variation related to reproduction and growth were explored over the lifespan of a single cohort of northern bay scallops, Argopecten irradians irradians (Lamarck), from September 1986 to April 1988 in the Niantic River estuary, Connecticut, USA. Analyses revealed that Gpi genotype explained an increasingly significant proportion of variation in scallop size (up to 15%) as the cohort aged. The genotype-specific effects were consistent across sampling dates and among measured traits. There was no evidence for heterosis with respect to size at this locus; however, rare genotypes contributed substantially to the relationship and showed some tendency to fall on the extremes of the phenotypic distribution. The strength and consistency of the genotypic effect on scallop size suggest that genetic variation for Gpi, or some locus in linkage disequilibrium with Gpi, may translate into biochemical and/or physiological variation and affect fitness in this species.