The African Clawed Frog Xenopus laevis, a global invader, exhibits a marked phylogeographic divergence among native populations in southern Africa, which seems to enhance its invasive potential. The polystomatid flatworm, Protopolystoma xenopodis, is the frog’s most frequently co-introduced metazoan parasite. In an integrative approach, we utilised morphometrics and molecular markers to assess variation in P. xenopodis in its native range. We measured twelve key morphological characters from 23 flatworms and compared these statistically between flatworms collected from the northern- and southernmost distribution in South Africa. Phylogenetic analyses were based on three concatenated markers, namely 28S and 12S rDNA and COX1, from six flatworms. The combination of five morphological characters, which involve egg size, gut morphology and size of the attachment hooks, differentiated northern and southern populations of P. xenopodis. The multilocus phylogenetic analyses showed a cluster of northern P. xenopodis and two southern lineages with more basal positioning. These findings demonstrate a relatively high level of intraspecific variation in P. xenopodis in its native range. The presented intraspecific variation of P. xenopodis could be potentially informative to trace geographic origin in its non-native range.