Evolutionary processes can complicate conservation efforts for species with uncertain taxonomic classifications and discrete geographic populations. Discordant morphological and genetic patterns across the geographic range of species further calls for the identification of evolutionary significant units for conservation. Using island and mainland populations of a small Australian passerine (the superb fairy-wren, Malurus cyaneus), we examine the relationship between morphological and genetic divergence among two subspecies, M. c. ashbyi (Kangaroo Island, South Australia) and M. c. leggei (South Australia, mainland), using eight microsatellite markers. Island birds showed clear evidence for morphological divergence, with a larger body size and thinner bill compared to mainland birds. Two genetic clusters were found using Bayesian methods, comprising mainland and island regions. Estimates of recent migration rates between all sites were very low (<2%). Morphological and genetic differentiation between island and mainland sites correlated significantly, but not when controlling for isolation by distance. Genetic and morphological substructure was evident with three distinct genetic clusters in each region. Males, the highly sedentary sex, appeared to drive correlations between morphological and genetic differentiation. Our study provides evidence that the subspecies classification of M. cyaneus in island and mainland regions encapsulates two independently diverging populations that can be recognised in conservation planning.