Mesopelagic organisms form huge biomass aggregations, supporting important pelagic trophic webs and several top predators. Although some studies on the occurrence, biology and ecology of these organisms are available, to date there are no investigations on their potential use for anticancer and antimicrobial biotechnological applications. The aim of this study was to screen extracts of seven mesopelagic species for possible anticancer (Lung cell line A549, skin cell line A2058, liver cell line HepG2, breast cell line MCF7 and pancreas cell line MiaPaca-2) and antibacterial (Gram-negative bacteria Escherichia coli and Klebsiella pneumoniae, the Gram-positive bacteria methicillin resistant/sensitive Staphylococcus aureus, and Mycobacterium tuberculosis) activities. Results showed that only two species were active, the lanternfish Myctophum punctatum and the Mediterranean krill Meganyctiphanes norvegica. In particular, M. punctatum showed strong activity against the A549 and MCF7 cells, while M. norvegica was more active against HepG2 cells. Regarding antibacterial assays, both species were active against methicillin resistant S. aureus. Fractionation and LC/MS dereplication of the fractions showed that the main compounds found in extracts of both species were EPA, DHA and ETA. For some of the detected compounds anticancer and/or antibacterial activity are already known, but this is the first time that such activities have been found for mesopelagic species.