The Australian and East Timorese species belonging to the truncatelloid family Stenothyridae are revised using molecular data and morphological characters from the shell, operculum, radula and external and reproductive anatomy. The Australian species Stenothyra australis is redescribed and two previously recognised subspecies are shown to be synonyms. The New Guinean species Stenothyra paludicola van Benthem Jutting, 1963 is redescribed and recorded from the Torres Strait region of northern Australia, and two new subspecies of S. paludicola are described from the Northern Territory and East Timor; S. paludicola topendensis n. subsp. and S. paludicola timorensis n. subsp. respectively. Stenothyra gelasinosa n. sp. is described from Australia, comprising three allopatric subspecies; S. gelasinosa gelasinosa n. sp. and n. subsp. from the eastern seaboard, S. gelasinosa phrixa n. subsp. from northern Australia and S. gelasinosa apiosa n. subsp. from the Pilbara region of Western Australia. Stenothyra frustillum is considered a nomen dubium. Molecular phylogenetic analysis of these taxa and other Asian stenothyrids supports these systematic decisions and provides a preliminary interpretation of relationships within Stenothyridae.