Eight highly variable microsatellite loci were used to examine the genetic variability and differentiation of grey seals (Halichoerus grypus) at two widely spaced British breeding colonies. Samples were collected from adults and pups on the island of North Rona, off the north-west coast of Scotland, and on the Isle of May, situated at the mouth of the Firth of Forth on the east coast Highly significant differences in allele frequencies between these two sites were found for all eight loci, indicating considerable genetic differentiation. Thus, although grey seals are known to range over very large areas outside the breeding season, site fidelity of adults and philopatry of pups for these breeding colonies must be sufficiently common to have effects, through genetic drift, at the sub-population level. Migration rate was estimated using Wrighf's fixation index (FST), Slatkin's private alleles model and the new statistic, RST, which is analogous to (FST) but which takes into account the process of microsatellite mutation. An almost 8-fold discrepancy between the values we obtained provides cautionary evidence that microsatellite loci may contravene one or more of the assumptions on which these methods are based.