The genetic structure of mussel recruits on a rocky shore in Nova Scotia was measured after a rare ice-scouring event which completely removed the intertidal community. Genotype frequencies were measured at three enzyme loci, phosphoglucose mutase (PGM), aminopeptidase-I (product of the leucine aminopeptidase (LAP) locus), and mannose phosphate isomerase (MPI), using cellulose acetate gel electrophoresis. The developing mussel assemblage was a mixture of Mytilus trossulus, M. edulis and their hybrids, with a greater proportion of the former species. Mussel settlers were collected for two years to examine whether genetic heterogeneity existed within and between cohorts of settlers. Settlement of mussels of both species began in April or May and continued into January. Temporal genetic heterogeneity was observed among groups of settlers, resulting from both variations in the relative proportions of the two species and from genetic heterogeneity within M. trossulus. Allele frequencies of mussel cohorts were followed from settlement to ten months post-settlement to investigate the possibility of species-specific selection and of genotype-specific selection within M. trossulus. Temporal genetic heterogeneity primarily was attributed to changes in the proportions of each species, indicating that post-settlement processes were species-specific. Early post-settlement changes were inconsistent, but later changes were clearly directional, resulting in decreased proportions of M. edulis in larger mussels in both years. There was some evidence of genotype-specific post-settlement mortality within M. trossulus, particularly during the early post-settlement period. Our results indicate that temporally variable settlement patterns and post-settlement selection interacted to produce temporal genetic heterogeneity in this mussel assemblage.