Forficulina, the largest suborder of Dermaptera (earwigs), has eight families. In five families (Pygidicranidae, Diplatyidae, Anisolabididae, Apachyidae, and Labiduridae), the males have two penises, whereas the males of the other three families (Spongiphoridae, Chelisochidae, and Forficulidae) have a single penis. Several cladograms have been proposed for Forficulina. However, those systems are constructed mainly from observations of male genital morphology and outstandingly inconsistent. This study reconstructed an earwig phylogeny with representatives of seven families (excluding Apachyidae) by using partial sequences of the mitochondrial 16S and nuclear 28S rRNA genes, sequences that are independent of genital evolution. To avoid difficulties caused by outgroup-rooting for a deep phylogeny, ingroup relationships were first established as unrooted trees based on the 16S, 28S, and combined data sets. The resulting affinities of the earwig families supported several superfamilies, such as Forficuloidea (single-penis families) and Pygidicranoidea (Pygidicranidae Diplatyidae). Inclusion of the outgroup (Glylloblattodea and Blattodea) did not distort the established ingroup relationships. However, the root position varied according to the genes and outgroup taxa used. Kishino–Hasegawa tests based on the maximum likelihood criterion suggested that the common ancestor of contemporary Forficulina had twin penises, each with one gonopore.