Although knowledge of the bioactive compounds produced by species inhabiting coastal waters is increasing, little is known about the bioactive potential produced by marine species occupying deeper habitats with high biodiversity and productivity. Here, we investigate about the bioactive potential of molecules produced by species that inhabit the crinoid beds, a poorly known essential fish habitat affected by trawling, wherein large amounts of commercial and noncommercial species are discarded. Based on a trawl survey conducted in 2019, 14% of the 64 species discarded on crinoid beds produce molecules with some type of bioactive potential, including; soft corals (Alcyonium palmatum); tunicates (Ascidia mentula); bony fish, such as horse mackerel (Trachurus trachurus); European hake (Merluccius merluccius); and chondrichthyans, such as small-spotted catshark (Scyliorhinus canicula). In addition, 16% of the discarded species had congeneric species that produce compounds with bioactive potential, indicating that such species might also possess similar types of bioactive molecules. Molecules with antioxidant, antitumour, antihypertensive, and antibacterial properties were the most frequent, which could provide the basis for future research aiming to discover new marine-based drugs and compounds for other human uses. Among all species or genera that produce compounds with bioactive potential, 68% presented medium or high vulnerability to trawling. Results show that the discarded catch contains many species, which produce different bioactive compounds that represent an added-value resource. These results highlight the importance of manage properly crinoid beds, to ensure that species that produce molecules with bioactive potential inhabiting these habitats are protected.