The genus Gomphandra Wall. ex Lindl. was studied and revised to more accurately reflect the diversity of the group. Floral morphology and fruit anatomy were compared to other genera of Stemonuraceae to assess reproductive diversity within the family and identify potential synapomorphies. Seven genera of Stemonuraceae possess what appears to be a unique fruit type: a laterally compressed drupe with fleshy appendage that aids in dispersal. Fruit of nine genera were sectioned, and all exhibit sclerified longitudinal bundles in the inner mesocarp; one bundle, which appears bright in cross-section under polarized light, may be a synapomorphy for the family. Seed coats are vascularized with a chalazal/post-chalazal bundle (7 genera) or a pachychalazal bundle (2 genera). Molecular data were sampled from four gene regions ( rbcL, trnL intron, trnL-F spacer, matK) in 10 species of three genera (Gomphandra, Grisollea, Stemonurus), for a total of 24 new sequences. Preliminary evidence suggests Grisollea and Codiocarpus (both with a laterally compressed fruit) are more closely related to each other than to Stemonurus or Gomphandra, which have uncompressed fruits. Members of Stemonuraceae may have a molecular synapomorphy in a 100 base pair region of TA repeats in the trnL-F spacer that is apparently not shared with any genera outside the family. Gomphandra has two moderately supported clades, one with the synapomorphy of terminal (vs. axillary) inflorescences. The revision of the genus recognizes 62 taxa: 56 species, three subspecies, and three varieties. Diversity is highest in the Philippines (17 taxa), followed by Borneo and Papua New Guinea (10 taxa each), and Sumatra (9 taxa). Twenty-nine new taxa are described, three species are resurrected, one species is reduced in status, and five taxa are synonymized. Problems with typification and nomenclature are corrected for 24 species of Gomphandra and six species in four other genera of Stemonuraceae.