We measured N₂ fixation rates and identified diazotrophic phylotypes in the mesopelagic layer along a transect spanning from New Caledonia to French Polynesia. N₂ fixation rates were low but consistently detected across all depths and stations. A distinct diazotrophic phylotype dominated at 650 dbar, coinciding with the oxygenated Subantarctic Mode Water (SAMW) and suggesting that the distribution of aphotic diazotroph communities is to some extent controlled by water mass structure.