Four new species of Rugopharynx Mönnig, 1927 are described from macropodid marsupials in Australia, some identified initially using molecular methods. Rugopharynx thetidis n. sp. from Thylogale thetis (Lesson) was initially included within R. sigma Chilton, Beveridge & Andrews, 1993 but was identified as being distinctive using molecular methods and is differentiated morphologically from R. sigma by the more anterior position of the deirid and by the distinctive curvature of the spicule tips. Rugopharynx thylogale n. sp., also from Thylogale thetis, is distinguished by the extreme elongation of the dorsal lobe of the bursa and spicule length (1.07-1.23 mm). Rugopharynx solitarius n. sp., again from Thylogale thetis, was initially included within Rugopharynx zeta (Johnston & Mawson, 1939) but differs morphologically in the features of the bursa. Rugopharynx disiunctus n. sp. from Macropus fuliginosus (Desmarest) was initially included within Rugopharynx rho Beveridge & Chilton, 1999 but was identified as distinctive based on DNA sequence differences. The new species differs from R. rho in the pattern of striations on the buccal capsule and in the lengths of the spicules. Additional records of species of Rugopharyx in M. fuliginosus in Western Australia are provided.