A multidisciplinary approach is an extremely powerful tool for determining genomic diversity and establishing genomic relationships within and among species. This study used cytogenetics and a molecular method (ITS of the rDNA) to uncover genomic diversity in Glycine canescens and Glycine tomentella and to establish their phylogenetic relationships with the other diploid species of the genus Glycine. Cytogenetics revealed that G. canescens accessions (PIs 583944, 583946, 583953, and 591575) from Western Australia were genomically similar. However, they were differentiated by a paracentric inversion from the standard G. canescens (PI 440932) collected from South Australia. By contrast, G. tomentella (2n = 40) accessions from Western Australia were highly diverse genomically. Cytogenetics and ITS investigations separated the diploid G. tomentella accessions in Australia into four distinct groups. The genome symbols DD (isozyme group D3; PI 505222), D1D1 (isozyme group D5; PI 505301), D2D2 (isozyme group D5; PI 505203), and D3D3 (isozyme group D4; PI 441000) are being assigned to these four groups. The D1 and D2 genome group accessions are distributed in Western Australia. The D3-genome group of G. tomentella accessions are morphologically similar neither to A-genome species nor to the D-, D1-, or D2-genome groups. However, the D3-genome group was phylogenetically grouped with the A-genome species, while the D-, D1-, and D2-genome groups showed a close relationship with E-, H-, and I-genome species. This study demonstrates that diploid G. tomentella of Western Australia is a complex species, and from an evolutionary viewpoint, it is actively radiating out into several genomic variants.Key words: Glycine spp., soybean, genome, cytogenetics, ITS region.