Abstract
<title>Abstract</title> <p> Cryptobenthic fishes, an important component of coastal ecosystems, are strongly dependent on the substratum and sensitive to small environmental changes, which makes them potential ecological indicators. Yet their assemblages remain poorly known in the eastern Mediterranean. This study examines the ecological preferences of cryptobenthic fishes and evaluates the assemblage composition they form across habitat types within the EUNIS habitat classification and identifies species with indicator value for particular habitats. Assemblages were surveyed by underwater visual census along timed transects between 0 and 40 m depth in Saros Bay (northern Aegean Sea; 40.32–40.62° N, 26.12–26.83° E) and Gökova Bay (southern Aegean Sea; 36.80–37.02° N, 27.44–28.26° E), Türkiye, during July–October 2022–2024. Thirty-eight species in four families (Gobiidae, Blenniidae, Tripterygiidae, Gobiesocidae) were recorded; <italic>Gobius geniporus</italic> and <italic>Gobius vittatus</italic> were the most frequent species in both bays. Composition was structured by both EUNIS habitat group and depth zone, with depth as the stronger axis. Species richness, diversity and evenness did not differ among habitats or depth zones, indicating that the habitat signal resided in species identity and relative abundance rather than in diversity. Thirteen candidate indicator species were identified, but these were bay-specific, with the same habitat group characterised by different species in each bay. Richness was lowest on bare soft sediments and highest in coralligenous habitat in Gökova, and on infralittoral rock in Saros. Although both bays contained a marine protected area (MPA), composition did not between protected and unprotected areas. </p>