Two monorchiid species are reported from the freckled goatfish, Upeneus tragula Richardson, from Moreton Bay, Queensland, Australia. Specimens of a species new to science were most morphologically similar to species of the genus Timonia Bartoli & Prevot, 1966, but significant differences in the arrangement of the testes (symmetrical vs oblique) and morphology of the terminal organ (bipartite vs unipartite) necessitate the proposal of a new genus; Madhavia n. g. is proposed for M. fellaminutus n. sp. Specimens of the second species are identified as Parachrisomon delicatus (Manter & Pritchard, 1964) Madhavi, 2008, extending its known range from Hawaii to Australia. Complete ITS2 and partial 28S rDNA sequence data were generated for both species and analysed with those for other monorchiids available on GenBank. Phylogenetic analyses of the 28S rDNA dataset showed that both genera are distinct from other sequenced monorchiids, but overall the resolution between genera is poor and more sequence data are required to elucidate relationships within the family. We propose to transfer Timonia stunkardi (Ahmad, 1985) and Timonia vinodae (Ahmad, 1987) to the genus Neotimonia Madhavi, 2008, as Neotimonia stunkardi (Ahmad, 1985) n. comb. and Neotimonia vinodae (Ahmad, 1987) n. comb. Additionally, we were unable to locate any literature on Parachrisomon brotulidorum (Toman, 1973) Madhavi, 2008 and consider this species as nomen nudum.