The taxonomic framework of the Haploporidae is evaluated and the relationships within the Haploporinae are assessed for the first time at the generic level using molecular data. Partial 28S and complete ITS2 rDNA sequences from representatives of six of the nine recognised genera within the Haploporinae were analysed together with published sequences representing members of two haploporid subfamilies and of the closely related family Atractotrematidae. Molecular analyses revealed: (i) a close relationship between the Atractotrematidae and the Haploporidae; (ii) strong support for the monophyly of the Haploporinae, Dicrogaster and Saccocoelium, and the position of Ragaia within the Haploporinae; (iii) evidence for rejection of the synonymy of Saccocoelioides and Lecithobotrys and the validity of the Dicrogasterinae; and (iv) support for the distinct status of Saccocoelium in relation to Haploporus. The wider sampling within the genera Dicrogaster and Saccocoelium confirmed the distinct status of the included species, thus rejecting previously suggested synonymies. Saccocoelioides, recently transferred to the Chalcinotrematinae, was nested within the Haploporinae and this was largely associated with the position of Forticulcita, resolved as the most basal haploporine genus. Forticulcita also possesses a well-delimited eversible intromittent copulatory organ, a feature unique in the Haploporidae which has not been previously considered an important apomorphy. This, in association with the present hypothesis of the Haploporinae based on molecular data, led us to erect Forticulcitinae subf. n. for Forticulcita; this resolved Saccocoelioides and, by extension the Chalcinotrematinae, as sister groups to the Haploporinae.