Accurate species identification is crucial for ecological studies. For copepods, this is usually based on a few diagnostic morphological characters, which can be highly conserved, resulting in an underestimation of species diversity in many copepod families. We elucidate species richness in the morphologically challenging and ecologically important deep-sea copepod family Spinocalanidae in the tropical Atlantic by applying an integrated taxonomic approach combining morphology, DNA-sequence analyses and proteomic fingerprinting. In total, 28 morphospecies could be discriminated, while 39 putative species were detected using DNA-sequence analyses and 42 using proteomic fingerprinting. This outcome verifies proteomic fingerprinting to simplify and accelerate future biodiversity studies of copepods with high taxonomic resolution. Our findings demonstrate the power of this integrated morphological and molecular taxonomic approach by revealing high numbers of cryptic or pseudocryptic species and thus uncovering the incompleteness of taxonomic guides for this group in the poorly explored mesopelagic realm. Furthermore, our analyses reveal a close relationship of Mospicalanus and Spinocalanus group A and indicate that the genus Spinocalanus may be polyphyletic. The underestimated species diversity suggests complex ecological interactions in terms of predator–prey relationships, interspecific competition and species-specific specializations in the vast, but under-studied mesopelagic realm.