Aglaia elaeagnoidea is the most widespread and one of the more morphologically diverse complex species in the largest genus of the mahogany family (Meliaceae, Sapindales). We performed maximum parsimony, maximum likelihood and Bayesian analyses (nuclear ITS rDNA) to estimate genetic relations among samples of Aglaia elaeagnoidea, and their phylogenetic position within Aglaia (more than 120 species in Indomalesia, Australasia, and the Pacific islands). Based on 90 accessions of Melioideae (ingroup) and four taxa of Cedreloideae (outgroup), this study 1) provides a first assessment of the genetic diversity of Aglaia elaeagnoidea; 2) investigates the geographic structure of the data in selected eastern and western regions of its distribution; and 3) suggests that Australia has been colonized only recently by A. elaeagnoidea and other species within the genus (Miocene/Pliocene boundary to Pliocene). Based on DNA data, morphology and additional evidence derived from biogenetic trends (secondary metabolites), the name Aglaia roxburghiana could be reinstated for specimens from the western end (India, Sri Lanka), but we have no data yet to indicate definitely where A. roxburghiana ends and A. elaeagnoidea begins either morphologically or geographically. Viewed in a more general context, Aglaieae are an ideal model group for obtaining more insights into the origin and evolution of Indomalesian and Australian biotas.