Synodontis catfishes in Lake Tanganyika have undergone a modest radiation, with differences among species in reproductive strategies, including one species that has evolved to be an obligate brood parasite. Here, we provide insights into the reproductive traits and histology of male and female reproductive organs of five Lake Tanganyika Synodontis species (S. irsacae, S. melanostictus, S. multipunctatus, S. petricola and S. polli). We describe the structures employed in oogenesis, spermiogenesis and spermiation. We show that the shape and size of the urogenital papilla is a valuable trait for sex determination in all species except S. polli, where the imprecision reached > 20 %. From a histological perspective, the inter-specific structural differences associated with the type of reproductive strategy were not found in the ovaries. However, testicular histology indicated variations in spermiation structures among species, namely in S. multipunctatus and S. irsacae. The differences identified may be related to variation in reproductive strategies among species. In particular, weaker eosinophily of testicular secretions was found in S. multipunctatus than in other species, suggesting the possibility of a different composition. Experimental manipulation of environmental and hormonal stimuli represents a promising direction for further research into the structural and functional diversity of male gonads in Synodontis species from Lake Tanganyika.