ABSTRACT: Eight microsatellite markers were used to screen over 1700 individual pearl oysters Pinctada maxima from 5 Western Australian (Lacepedes, 80 Mile Beach Shallow, 80 Mile Beach Deep, Port Hedland and Exmouth Gulf), 1 northern Australian (Darwin) and 2 Indonesian (Madura and Sumbawa) populations. There was a strong and highly significant relationship between the amount of genetic divergence between pairs of populations and their degree of geographical separation. Within Australia, there was some indication for genetic differences between Exmouth Gulf and the other Western Australian populations and also between Darwin and the Western Australian populations. The Indonesian populations were significantly different from all Australian populations, suggesting little or no direct recruitment to Western Australia from Indonesian sources. Comparison of 2 year-classes of spat (0+ and 1+) in some Australian populations showed no evidence of differences among Western Australian sites. Comparison of the same recruitment class at 2 different ages (0+ spat in 1998 and 1+ spat in 1999) provided no evidence for selection at the screened, or closely linked, loci. With the possible exception of Exmouth Gulf, Western Australian populations can be considered 1 stock with a large effective population size (no <300 and more likely several 1000s).