Leucine aminopeptidase (LAP) belongs to a family of ubiquitous peptidases, with roles in growth and development, stress responses and adaptation to changing environmental conditions. The LAP gene was sequenced from a commercially important marine bivalve: the Pacific oyster Crassostrea gigas, and sequence polymorphisms were identified. This study identified 21 single nucleotide polymorphisms (SNPs), which would alter the encoded amino acid sequence, one 3 base deletion, one single base deletion, which would create a truncated protein (predicted to be nonfunctional), and a further 50 silent SNPs. The 23 polymorphisms altering protein sequence were found to occur in 34 different combinations, which we designated as 34 alleles: many more than the 6 alleles predicted previously by allozyme analysis. Predictions of protein structure and stability were used to identify which of the changes in the protein sequence are most likely to affect enzyme function. The sequence of the LAP gene noncoding regions was also analyzed and simple sequence repeats (microsatellites) were found in introns 1 and 9. The intron 1 microsatellite region was also found in another species of oyster: Crassostrea hongkongensis. We have demonstrated that the LAP gene region of the Pacific oyster, C. gigas is highly variable, and have identified new, potentially useful, genetic markers.