Lake Tanganyika is an aquatic biodiversity hotspot with the most diverse cichlid species assemblage of all African lakes. This makes it an important and remarkable study area for biologists. Whereas over 20 monogenean species were described from littoral cichlids, the biodiversity of these ectoparasitic flatworms in the depths is almost unexplored. Our host dataset comprised 82 individuals from 12 cichlid species belonging to four tribes (Bathybatini, Trematocarini, Benthochromini, Limnochromini) occurring in the deepwater habitat. Samples originated from localities throughout the lake. A wide range of techniques and analyses was used to describe their monogenean infection from a morphological as well as a genetic point of view. Finally, 849 monogenean individuals from 8 host species were collected. Three different species belonging to Cichlidogyrus were distinguished. Members of the Bathybatini are infected by a single species, C. casuarinus. According to previous studies, a decrease of parasite host specificity is probably correlated with lower host availability in the deepwater realm. Whereas significant differences in C. casuarinus morphology correlated with host preference, no incipient speciation was observed in the genetic part of the study. Moreover, analyses based on 42 mitochondrial COI fragments suggest a recent population expansion of C. casuarinus. The cichlids Trematocara unimaculatum and Benthochromis horii host two different Cichlidogyrus species, belonging to different lineages. Our study illustrates the potential of ectoparasites as a tool to reveal basic evolutionary principles as well as host species interactions.