Identification of specimens belonging to the genus Linguatula (Pentastomida) is relatively easy due to their unique morphology. However, differentiation between species of Linguatula can be challenging for several reasons, including considerable differences between different developmental stages of the parasite within and between species. Currently, 18S rRNA and Cox1 sequences are the only available comparable sequences in GenBank, but recent research has discussed the utility of 28S rRNA for pentastomid phylogenetics. This study presents 28S rRNA gene sequences for two members of the genus Linguatula. Sequences of 28S rRNA were successfully obtained from well-identified samples of L.serrata (collected in Australia) and L.nuttalli (collected in South Africa), with voucher specimens. Phylogenetic analysis of the 28S rRNA region showed 6% difference between L.serrata and L.nuttalli, with low levels of intraspecific variation. In comparison, 18S rRNA and Cox1 sequences from the same specimens showed 0.23% and 13% interspecific differences, respectively. The results of this study show that 28S rRNA has greater genetic diversity to allow for improved differentiation between species of Linguatula than 18S rRNA but is on par with Cox1. Records that do not provide adequate morphological or molecular data to justify independent specific diagnoses must be regarded cautiously, and the need for continued research on species of Linguatula, using a combined morphological and molecular analysis, across a number of different hosts, development stages, geographical regions and molecular markers is highlighted.