In 2013 and 2016, a total of 284 cichlid individuals belonging to 43 Tanganyikan species were collected from the Burundese and Congolese lakeshores, and examined for gill ectoparasites. Morphological and molecular identification of the gill monogeneans were performed, and phylogenetic analyses were carried out by employing different molecular markers (28S rDNA, 18S rDNA and ITS-1). Trees were generated using maximum likelihood and Bayesian inference algorithms. The taxonomic study of more than 800 Cichlidogyrus specimens has demonstrated the occurrence of 37 monogenean species. These numbers include 11 Cichlidogyrus species previously described on Tanganyikan cichlids and 14 species that are considered new for science. Our investigation represents the first parasitological examination of representatives belonging to the Tanganyikan cichlid genera Aulonocranus, Callochromis, Cyphotilapia, Cyprichromis, Eretmodus, Tanganicodus, and Xenotilapia. Congolese Aulonocranus dewindti hosted two new Cichlidogyrus species exhibiting similar morphotypes as those monogenean species reported recently on the same host in Burundi. Likewise, a few Cichlidogyrus species have already been recognized on the gills of Petrochromis spp., but no formal description has been provided yet. Our study allowed us to record 7 new Cichlidogyrus species on Congolese specimens of Petrochromis. Furthermore, the gills of Tylochromis polylepis revealed the presence of C. sp. “T. polylepis 3”, an undescribed species already reported from the same host. We provide a morphological characterization of the hard parts to this species. Finally, phylogenetic trees show that all Cichlidogyrus are grouped together following the phylogeny of their Tanganyikan cichlids, and mirror the affinities revealed by morphological characters within monogenean species and among their fish hosts.