The phylogenetic relationships among selected species and genera of Gerrinae (Heteroptera: Gerridae) were investigated in a parsimony analysis of 2268 bp of DNA sequence data from the genes encoding COI+II, 16S rRNA and 28S rRNA. The taxa represented 12 of 15 recognized genera of Gerrinae and with outgroup taxa from all other subfamilies of Gerridae, including three of five recognized genera of Eotrechinae, which is considered the sister-group of Gerrinae. The resulting phylogeny shows that Gerrinae is not monophyletic, since a clade comprising Gerris, Aquarius, Limnoporus, Tachygerris, Eurygerris and Gigantometra is more closely related to representatives of the subfamily Eotrechinae than to a clade comprising Limnogonus, Neogerris, Limnometra, Tenagogerris and Tenagogonus. The two currently recognized gerrine tribes, Tachygerrini and Gerrini, were also paraphyletic, since Eurygerris was sister-group to Gigantometra, while Tachygerris was sister-group to Limnoporus + Aquarius + Gerris. Limnogonus and Neogerris were found to be strongly supported sister-taxa, and their sister-group was a clade comprising Limnometra, Tenagogerris and Tenagogonus, none of which were monophyletic. Finally, Aquarius chilensis (Berg, 1881) was sister-group to a clade comprising Aquarius amplus (Drake & Harris, 1938), A. remigis (Say, 1832) and A. remigoides (Gallant & Fairbairn, 1993), recognized as the A. remigis species group, and the entire clade was sister-group to Gerris. Based on the phylogenetic reconstruction, we outline possible diagnostic character combinations for a future revision of the Gerrinae and discuss the fossil record. While some of the relationships reinstate earlier ideas, e.g., Limnogonus and Neogerris being sister groups, many others are poorly supported and poorly diagnosed, and therefore, we retain from drawing taxonomic conclusions until data is available from the remaining genera, which can support a future generic revision of the Gerrinae. The updated checklist of species assigned to the subfamily is therefore based on the established taxonomy.