Divergence in sexually deceptive orchids is thought to occur through shifts in the attraction of specific pollinators, a process that is mediated by changes in the floral odours that lure sexually excited male insects. We investigated the origin of reproductive isolation in a sexually deceptive species complex of Chiloglottis R.Br. (Orchidaceae: Diurideae). Two geographically separated montane regions in eastern Australia were sampled, each containing sympatric pairs of orchid taxa presently found under the name, Chiloglottis pluricallata. Behavioural tests confirmed at least three distinct orchid taxa that specifically attract different pollinators. An artificial crossing experiment among two taxa from one region demonstrated their interfertility, and confirmed isolation to be a function of pollinator attraction. A phylogeographic analysis using amplified fragment length polymorphisms (AFLPs) indicated that samples from each geographical region are most closely related, a pattern consistent with in situ or sympatric divergence. However, an extensive population genetic study on two taxa from one region failed to entirely reject the possibility of intertaxon gene flow. Although clear genetic differentiation of the taxa is evident in two out of three sites where both grow in direct sympatry, overall, the two taxa are not strongly distinguished by AFLP markers. The reconstruction of a simple bifurcating pattern of divergence may be confounded by a combination of contemporary population-level processes operating within each taxon, the retention of ancestral polymorphism or intertaxon gene flow.