Anatomic and cytological studies of some 110 species of deep‐sea eels of among others the families Congridae, Colocongridae, Heterenchelyidae, Synaphobranchidae, Nettastomatidae, Nemichthyidae, Serrivomeridae, revealed a very high diversity in the visceral organs, especially gonads, guts and kidneys and their relation to the anal opening.The ovaries of various species were either monocyclic, producing eggs periodically, or polycyclic with frequent egg production. Some testes showed synchronous and others asynchronous sperm production. In some of the families, such as Heterenchelyidae, all the gonads are situated post‐anally, in the tail, whereas in Congridae the extent of penetration varies in the different genera, indicating that this family is an artificial one. As some gonads of a few species were found to harbour gametes of the two sexes, the possible occurrence of hermaphroditism is discussed. Melanization of gut was observed in numerous species produced by the penetration of pigmented tissue between the muscle layers of the gut wall or between these and the gut epithelium, this differing between various taxa and in young and adult specimens. The melanization of gut or parts of gut prevent slight (emitted by the swallowed bioluminescent prey) from being seen outside, and in this way protects the eel from predation. Pigmentation also occurs in the kidneys and other explanations for melanization are therefore discussed. In numerous species the gut, kidney and gas chamber partially penetrate into the tail, and as with the gonads, these characters can also be used on eel taxon