Pontomyia (Diptera : Chironomidae) is an exclusively marine and flightless insect genus with four described species from the Indo-Pacific and one undescribed taxon known only by its larvae, pupal skins and females from the western Atlantic. A previous study of relationships among three of the Indo-Pacific species reported each of them to be monophyletic, with high genetic diversity within P. natans Edwards, 1926, the type species, and P. pacifica Tokunaga, 1932. The evolutionary affinities of the Australian endemic P. cottoni Womersley, 1937, which resembles P. natans, as well as the putative Atlantic species are hitherto undetermined. A complete molecular phylogeny of the genus based on two nuclear and two mitochondrial DNA markers indicates that P. cottoni and a Puerto Rican (Atlantic) larval population are nested within the P. natans clade. Furthermore, P. natans and P. cottoni are inseparable in all morphological characters used previously to distinguish them. Therefore, we synonymise P. cottoni with P. natans, syn. nov., whose known range now encompasses all three ocean basins after including the Puerto Rican population. This distribution warrants further investigation into the life history of Pontomyia, a midge with one of the shortest known adult lifespans among insects.