Nile tilapia, one of the most popular aquaculture species worldwide, has been introduced into the Congo Basin several times for aquaculture purposes. Previous studies based on morphological features showed that some of the monogenean gill parasites were co-introduced with Nile tilapia and some spilled over to native Congolese cichlids. In this study, we genetically investigated the co-introduced monogeneans of Nile tilapia from three major parts of the Congo Basin: Upper, Middle and Lower Congo. We sequenced 214 specimens belonging to 16 species of Monogenea, collected from native and introduced tilapia species from Congo, Madagascar and Burundi. We evaluate their position in a phylogeny including 38 monogenean species in total. Our results confirm the co-introductions in the Congo Basin and suggest one unreported parasite transmission from introduced Nile tilapia to native Mweru tilapia in Upper Congo, which was undetectable with a morphological study alone. Shared parasite COI haplotypes between Madagascar and the Congo Basin illustrate how anthropogenic introduction events homogenize parasite communities across large geographical distances and thereby disrupt isolation by distance patterns. Contrary to our expectation, the parasite populations co-introduced in the Congo Basin reveal a high COI diversity, probably resulting from multiple Nile tilapia introductions from different geographic origins. Additionally, we tested the barcoding gap and the performance of mitochondrial COI and nuclear ribosomal ITS-1, 28S and 18S markers. We found a significant barcoding gap of 15% for COI, but none for the other markers. Our molecular results reveal that Cichlidogyrus halli, C. papernastrema, C. tiberianus, C. cirratus and C. zambezensis are in need of taxonomic revision.