With the aim to solve long-standing problems of taxonomic delimitation within the E. obovatus species complex (E. obovatus G.Don, E. arnhemicus F.Muell., E. sp. Mt Bellenden Ker (L.J.Brass 18336) Qld Herbarium and E. coorangooloo J.F.Bailey & C.T.White), diversity and relatedness were assessed using a combined population genetics and morphometric approach among 181 and 102 individuals respectively. Simple sequence-repeat (SSR) markers were analysed with clustering methods, analysis of molecular variance (AMOVA) and STRUCTURE. The morphometric data were analysed using cluster and classification and regression tree (CART) methods. The morphometric and genetic analyses together resolve discrete groups corresponding to E. arnhemicus, E. coorangooloo, E. obovatus and E. sp. Mt Bellenden Ker. Elaeocarpus arnhemicus is clearly distinct from all other entities on most of the morphometric and genetic analyses. By contrast, E. sp. Mt Bellenden Ker and E. obovatus were not clearly separated from each other in many morphometric analyses, but can be distinguished clearly by the strongly curved pedicels in early bud and hairy ovary, and, to a lesser extent, by the frequent occurrence of two racemes per axil and cuneate leaf bases, and on the results of the genetic analyses. Elaeocarpus coorangooloo exhibits considerable genetic admixture with the other entities, but it is morphologically distinct. SSR profiles suggested that E. arnhemicus and E. obovatus may be tetraploid, whereas the other entities are diploid. This study has clarified the taxonomic limits of the currently recognised species E. arnhemicus, E. obovatus and E. coorangooloo and supports recognition of E. sp. Mt Bellenden Ker at subspecies rank, described herein as E. obovatus subsp. umbratilis Y.Baba & Crayn. A key to all taxa and revised accounts of E. arnhemicus, E. obovatus subsp. obovatus and E. coorangooloo are provided.