The functional diversity of echinoderms has been understudied, even though these organisms are critical components of various ecosystems, including coral reefs and hard-bottom benthic communities. Additionally, there are only a few papers relating the protection level of marine protected areas (MPAs) with functional diversity. In this study, we calculate the functional diversity of echinoids and asteroids in 11 coral and rocky reefs with different protection levels across the Mexican Pacific. We recorded the abundance of 15 echinoderm species comprising seven echinoid and eight asteroid species. More than 30 morphological and ecological traits of the censused species were evaluated to calculate two functional diversity indices: Rao’s quadratic entropy index (FDQ) and functional richness (FRic). Latitudinal patterns of functional diversity differed between groups. Asteroids showed the highest FDQ and FRic values in the Gulf of California. Echinoids showed FDQ peaks at the highest (Bahia de los Angeles; 28° 56′, − 113° 30′), and the lowest latitude (Bahias de Huatulco; 15° 43′, − 98° 08′) sites. The Ixtapa-Zihuatanejo site (17° 39′, − 101° 36′) had the highest FRic values. Generalized linear mixed models showed that protection level did not have any significant effect on FDQ or FRic. Latitude, on the other hand, did have a significant effect on asteroid functional diversity, although no significant effects were found for echinoids. The lack of an effect of protection level, and the support of a latitudinal gradient in terms of both taxonomic and functional diversity, has important implications for conservation efforts, supporting the idea of a protected area network to maintain adequate regional biodiversity.