Conservation strategies, such as the establishment of Marine Protected Areas (MPAs), aim to safeguard biodiversity and to promote resilience of ecosystems by increasing their capacity to maintain key functions and processes following disturbance. However, the extent to which ecosystems in MPAs exhibit resilience remains debated. To address this question, we evaluated changes in reef fish species and functional diversity over time in relation to environmental and anthropogenic disturbances at multiple locations in the Gulf of California, Mexico. From 2005 to 2017, we assessed reef fish species richness and abundance in three MPAs: one no-take marine reserve (Cabo Pulmo) and two multi-use marine protected areas (MUMPAs: Espíritu Santo and Loreto). To examine change in functional diversity and composition, we calculated three functional diversity indices – functional richness, functional dispersion and functional originality – using six biological traits (size, mobility, period of activity, gregariousness, water column position, and diet). Species richness, density and functional diversity were maintained over time (resilience) in the no-take marine reserve. In contrast, MUMPAs showed temporal decline in species richness, which translated into decreases in functional richness and increases in functional dispersion. These differences were also observed at the species level: in Cabo Pulmo, only two ‘loser’ species declined in density, while Espíritu Santo and Loreto showed declines of 12 and 17 species, respectively. The two MUMPAs also shared 9 of the total 22 ‘loser’ species, which are generally abundant and common in the Gulf of California. Density declines were attributed to the combined effect of environmental (sea surface temperature and Chlorophyll-a anomalies) and anthropogenic (fishing, tourism and coastal population density) disturbances. Given the regional decline and the ecological importance of dominant species, long-term decreases in their populations can profoundly modify processes and reef ecosystem services in this region. Thus, local management strategies should be implemented to try to reverse the observed recent decline in fish diversity in MUMPAs.