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Wallacean island populations of two Vespertilioninae bats,Myotis muricolaandScotophilus kuhlii, which have similar geographical ranges, showed marked contrast in the amount and pattern of genetic variation. Within islands, genetic variation was on average much higher inM. muricolabut declined from west to east, whereas all populations ofS. kuhliihad uniformly low levels of genetic variation by mammalian standards.S. kuhliishowed little genetic differentiation between islands and estimates of gene flow were substantial whereas island populations ofM. muricoladiffered markedly and there was a strong isolation-by-distance effect associated with the extent of the sea crossing between islands. Furthermore, the lower mean heterozygosity and small genetic distances between eastern island populations ofM. muricolais evidence that there has been a bottleneck associated with the colonization of this area. The attenuation of genetic diversity to the east is also seen in some other mammalian species and may indicate limits to dispersal and have implications for species management. The patterns of variability inS. kuhliimay be a consequence of its strong dispersal capacity and close association with human activity, which, together with other factors, suggest a panmictic population. © 2004 The Linnean Society of London,Biological Journal of the Linnean Society, 2004,83, 421–431. [ABSTRACT FROM AUTHOR]