Molecular tools increasingly reveal cryptic lineages and species that were previously unnoticed by traditional taxonomy. The discovery of cryptic species in sympatry prompts the question of how they coexist in the apparent absence of ecological divergence. However, this assumes first that the molecular taxonomy used to identify cryptic lineages delimits species boundaries accurately. This issue is important, because many diversity studies rely heavily or solely on data from mitochondrial DNA sequences for species delimitation, and several factors may lead to poor identification of species boundaries. We used a multilocus population genetics approach to show that three mtDNA-defined cryptic lineages of the fig wasp Pleistodontes imperialis Saunders, which pollinate Port Jackson figs (Ficus rubiginosa) in north-eastern Australia, represent reproductively isolated species. These species coexist locally, with about 13% of figs (where mating occurs) containing wasps from two or three species. However, there was no evidence for gene flow between them. Confirmed cases of coexisting cryptic species provide excellent opportunities for future studies of the ecological and evolutionary forces shaping both species coexistence and fig/pollinator coevolution.