It has been established that cryptic fish (CF) contribute to keeping the equilibrium of marine environments, and are also potential indicators of the environment. In the present study, ecological evaluations of CF-associated with reef communities exposed to high or low anthropogenic pressure off the coast of Colima, Mexico (La Boquita-LB, and Carrizales Bay-CA, respectively) were carried out. ... [Show full abstract] During 2014 a total of 16 surveys were carried out during winter-spring (WS), and eight surveys were carried out in summer-fall (SF). Three CF surveys were carried out in each reef community, covering a 180 m2 area; several ecological indices were calculated, and the benthic habitat was characterized. A total of 3,056 CF belonging to 23 species, 22 genera, and 15 families were recorded. The species Axoclinus lucillae, Acanthemblemaria macrospilus, Coralliozetus boehlkei, Ekemblemaria myersi, and Hippocampus ingens represented new records for CA and LB. The physiographic and topographic characteristics of the marine substrate were factors that significantly influenced the occurrence of CF, especially those with reduced mobility. There was higher CF richness and diversity during the SF. The species A. macrospilus, C. boehlkei, and E. myersi, associated with rocky environments with high sponge and macroalgae cover, were identified as potential bioindicators of degradation of the benthic habitat. The species Cirrhitichtys oxycechalus, A. macrospilus, Coryphopterus urospilus, and Elacatinus punticulatus were associated with coralline, crystalline, and relatively unperturbed environments.