The dwarf galaxias (Galaxiella pusilla) and little galaxias (Galaxiella toourtkoourt) are both threatened freshwater fish from south-eastern Australia. Occasionally populations have been found with enlarged heads associated with the accumulation of ‘white balls’, but the cause of these deformities has not previously been investigated. In this study, histopathology and molecular techniques were employed to identify cysts extracted from the heads of Galaxiella species across six populations. Histopathology and DNA sequences from both mitochondrial (cytochrome c oxidase subunit I) and nuclear (ribosomal internal transcribed spacer 1) regions identified the cysts as metacercariae of Apatemon gracilis (Rudolphi, 1819), a cosmopolitan digenean trematode species. Heavy infestations of trematode metacercariae within Galaxiella populations are of concern due to the potential to cause increased mortality associated with altered behaviour of the fish host that increases the likelihood of predation. Direct mortality from infestations is also possible, but not quantified in this study.