Much attention is paid in conservation planning to the species concept to ensure comparability across studies and regions when classifying taxa against endangerment criteria and setting priorities for action. However, many authorities now accept taxonomic ranks below the species level and non-taxonomic intraspecific divisions to be factored into subspecies, key populations, evolutionarily significant units or designatable units. There are deeper reasons for clarifying species boundaries – interpretation of variation in traits across the landscape as a response to an environmental gradient can be seriously confounded by the presence of two or more cryptic species under study. Understanding phylogeographic patterns is a key component in the identification of such species boundaries and determination of substantial geographic structure within species. We interrogated genome-wide SNPs data sets and ML species trees to identify candidate species within B. duperreyi. We generated 12,532 reliable polymorphic SNP loci from 60 populations covering the distribution of B. duperreyi to assess gene flow and to define population structure in the form of diagnosable lineages. We identified five well-supported diagnosable operational taxonomic units (OTUs) of which two were regarded as putative species within B. duperreyi. The first species is distributed in the south-eastern high country including that in Tasmania. The second is an aggregation of diagnosable lineages (ESUs) occupying the lower elevation and coastal areas (including Kangaroo Island, the type locality for B. duperreyi). They have broadly parapatric distributions. Our study provides foundational work for the detailed taxonomic re-evaluation of this species complex and highlights the need for biodiversity assessment to include an examination of cryptic species below the species level. Such information on lineage diversity within species can be factored into conservation planning regardless of whether a decision is made to diagnose and describe new species taxonomically.