A survey of Indo-Pacific lutjanids of the subfamily Caesioninae revealed the presence of Siphodera gurukun Machida, 1910 and two new cryptogonimid taxa from off Heron and Lizard Islands on the Great Barrier Reef, Australia, Ningaloo Reef, Western Australia and Rasdhoo Atoll, Maldives. A combined morphological and genetic characterisation of these species shows that they form a clade distinct from the type-species of Siphodera Linton, 1910, S. vinaledwardsii (Linton, 1901), and warrants the proposal of a new genus. Here we propose Siphomutabilus n. g. and transfer Siphodera gurukun Machida, 1986 as the type-species, Siphomutabilus gurukun (Machida, 1986) n. comb. Siphodera aegyptensis Hassanine & Gibson, 2005 is transferred to Siphomutabilus as S. aegyptensis (Hassanine & Gibson, 2005) n. comb. based on morphological and ecological similarities. Siphomutabilus raritas n. sp. is described from Caesio cuning (Bloch) off Lizard Island and S. bitesticulatus n. sp. is described from Pterocaesio marri Schultz off Heron Island. The two new species are unique in that they have two testes, making their morphology broadly consistent with that of Metadena Linton, 1910, yet the molecular analyses conducted here indicates that they are unequivocally united with Siphomutabilus gurukun (which has multiple testes) to the exclusion of Metadena lutiani (Yamaguti, 1942), which was sequenced here. The dramatic phenotypic plasticity observed among such closely related species of Siphomutabilus suggests a secondary modification of what is generally considered a robust generic diagnostic character within this and other digenean families, highlighting the need for a combined morphological and molecular diagnostic approach when characterising these taxa. Siphodera Linton, 1910 is amended to include just two species, the type-species S. vinaledwardsii (Linton, 1901) Linton, 1910 and S. cirrhiti Yamaguti, 1970, which are distinguished by their lack of oral spines and multiple testes that are primarily extracaecal. Siphodera ghanensis Fischthal & Thomas, 1968 is considered a species incertae sedis here based on significant morphological and ecological differences compared with species of Siphodera and Siphomutabilus n. g.