A cohort of newly settled Mytilus edulis (L.) (Mollusca: Bivalvia) spat (mean shell length 530 µm) was collected from red filamentous algae at a site on the North Wales coast. After a period of growth in the laboratory, cellulose acetate and starch gel electrophoresis were used to investigate genotype frequencies at the Gpi, Odh, Lap, Pgm, Idh and Mpi loci. Individual testing of each locus, using the X2 test revealed significant deficiencies of heterozygotes at the Pgm, Mpi and Idh loci. However, further testing using a sequential Bonf erroni test, designed to assess the probability of observing at least one significant result from a number of tests by chance alone, revealed that only the deficiency of heterozygotes at Pgm and Mpi loci was significant at the table-wide 95% level. Since post-collection mortality was <3%, these heterozygote deficits must have existed at the time of collection. The conclusion drawn is that heterozygote deficiencies in mussels are generated during the larval stage or at early settlement.