The phylogeny of monogeneans of the genus Thaparocleidus that parasitize the gills of Pangasiidae in Borneo and Sumatra was inferred from molecular data to investigate parasite speciation. The phylogeny of the Pangasiidae was also reconstructed in order to investigate host-parasite co-evolutionary history. The monophyly of Thaparocleidus parasitizing Pangasiidae was confirmed. Low intra-species molecular variability was observed in three Thaparocleidus species collected from geographically distant localities. However, a high intra-species molecular variability was observed in two Thaparocleidus species suggesting that these species represent a complex of species highly similar in morphology. When comparing host and parasite phylogenetic reconstructions, distance-based as well as tree-based methods revealed a significant global fit between parasite and host phylogenies. Using different event costs schemes, parasite duplication (i.e. intrahost speciation) was recognized as the most common event in Thaparocleidus, while the numbers of cospeciation and host switches were lower and similar to each other. When collapsing nodes corresponding to duplication cases, our results suggest host-switches in the Thaparocleidus-Pangasiidae system precluding congruence between host and parasite trees. The morphometric variability of the parasite attachment organ was investigated and it was found that this variability is not linked to phylogeny, suggesting that the attachment organ is under adaptive constraint. We showed that haptor morphometry is linked to host specificity, whereby non-specific parasites display higher morphometric variability than specialists.