Cryptobenthic fishes were often overlooked in the past due to their cryptic lifestyle, so knowledge of their ecology is still incomplete. One of the most poorly studied taxa of fishes in the Mediterranean Sea is clingfish. In this paper we examine the habitat preferences of three clingfish species (Lepadogaster lepadogaster, L. candolii, and Apletodon incognitus) occurring in the Gulf of Trieste (Northern Adriatic). The results show that all three species have a cryptic lifestyle and are well-segregated based on their depth distribution and macro- and microhabitat preferences. L. lepadogaster inhabits shallow waters of the lower mediolittoral and upper infralittoral, where it occurs on rocky bottoms under stones. L. candolii similarly occurs in the rocky infralittoral under stones, but below the lower distribution limit of L. lepadogaster, and in seagrass meadows, where it occupies empty seashells. Such hiding places in seagrass meadows are also occupied by A. incognitus, which mostly occurs below the lower distribution limit of L. candolii. Despite the overlap of depth and macrohabitat, the probability of individuals of two species encountering each other or competing in the same habitat is low when the depth range is combined with the microhabitat preferences of these species.