The Indotropical freshwater mussel assemblage has more genera of uncertain subfamily-level position (i.e. genera incertae sedis) than all other regional faunas. Of the 16 genera incertae sedis in the Indotropics, only two, Harmandia and Unionetta, are distributed in the mainland southeast Asia subregion. Resolving the enigmatic systematic position of Harmandia and Unionetta would finally establish a complete subfamily-level classification for the freshwater mussel genera of southeast Asia and facilitate more comprehensive evaluation of regional freshwater mussel diversity and distribution. Molecular phylogenetic reconstructions using the nuclear–encoded large ribosomal subunit rRNA (28S) and the mitochondrial protein-coding cytochrome c oxidase subunit I (COI) recovered Harmandia and Unionetta in the Indo-Afrotropical subfamily Parreysiinae, and more specifically as members of the tribe Indochinellini (formerly Oxynaiini). Harmandia is shown to be polyphyletic with its former species belonging to three distantly related clades of the Unionoida (i.e. Parreysiinae, Rectidentinae and Hyriidae). Unionetta was likewise not recovered as monophyletic, despite the strong morphological similarities and close geographic proximity of the sequenced individuals. Based on a synthesis of molecular, morphological and biogeographic data, the taxonomy and geographic distributions of Harmandia and Unionetta are revised. These results are discussed in the context of the dispersal of the Parreyssiinae into Southeast Asia and the species-level diversity of the Indochinellini in the Mekong River.