Genetic diversity is considered essential for populations to adapt to a changing environment. Measures of genetic diversity to evaluate how isolated, inbred and viable a population is, are typically based on various neutral markers, such as microsatellites or mitochondrial DNA control regions. However, genetic diversity to guide conservation management is better reflected by coding regions of functionally important genetic loci, such as the major histocompatibility complex (MHC) genes. In this study we assessed population viability and MHC diversity of two bottlenose dolphin (Tursiops cf. aduncus) populations in Western Australia. From demographic data, the larger Shark Bay population appears to be stable, whereas the smaller Bunbury population was forecast to decline. Furthermore, we found the more viable Shark Bay population to be more genetically diverse for at least one (MHC II, DQB, exon 2) of the three MHC loci that we investigated. Our findings are consistent with the hypothesis that large, viable populations typically display greater genetic diversity compared to smaller, less viable populations. A larger population, such as the Shark Bay dolphin population, is thus potentially more robust to natural or human-induced changes to coastal ecosystems it inhabits across Australasia.