Mapping diversity hotspots of key species, such as the crop wild relatives, is an essential task for their conservation and for their further exploration. In this paper, we develop and apply methods to locate centres of species richness (SR), endemism, phylogenetic diversity and phylogenetic endemism (PE) for the Australian perennial diploid species of Glycine (Fabaceae). The study taxa are congeneric with the cultivated soybean Glycine max. The DNA sequence data for the phylogenetic analysis are histone H3D gene sequences for these Glycine species. The highest 2.5 % grid cell scores of diversity were defined as the Glycine diversity "hotspots". The hotspots for the four types of diversity are located in the Kimberley district Western Australia, the Wet Tropics and south-eastern Queensland. The observed frequency distribution of SR values were compared with a theoretical distribution that assumed a species-specific but geographically constant probability for the occurrence of each individual species. The comparison showed broad trends of geographic dispersion overlaying localised high diversity. Simulations of endemism scores supported these themes. No grid cell scored highly for all four diversity metrics, as each index captured specific types of diversity. The inclusion of phylogenetic data pinpointed new areas of biodiversity that were less obvious from other metrics. The Kimberley district emerged as a crucial centre of Glycine diversity with two related lineages of narrowly endemic species. Overall, ~16 % of the endemism centres, and 24 % of the PE centres are conserved in situ in protected areas.