We examined the relations between ¢tness-related traits of wild harbour seal (Phoca vitulina) pups with microsatellite heterozygosity, and with a measure of genomic diversity based on the mean squared distance between microsatellite alleles within an individual, mean d 2 . Birth weight was positively in£uenced by maternal age, pup sex, and either mean d 2 or individual heterozygosity in separate multiple regression models. The association of birth weight with mean d 2 was stronger than that with heterozygosity, however. The factors maternal age, pup sex, and mean d 2 combined to account for 36.8% of the variation in birth weight, with mean d 2 accounting for the greatest explanatory power (52.3% of the variance explained). Pups which survived until weaning had signi¢cantly higher mean d 2 than pups which died, independent of birth weight. These e¡ects are consistent with heterosis resulting from recent population mixing, and/or inbreeding depression in this population. Mean d 2 thus provides (i) a better measure of individual genetic variability than heterozygosity for microsatellite data; and (ii) a convenient tool for assessing the e¡ects of inbreeding and outbreeding in natural populations.