The skull often reveals adaptation to ecological and environmental influences. Food availability affects the somatic growth of otariids, and population abundance can influence male intrasexual competition. We hypothesized there would be regional differences between Galapagos sea lion (GSL, Zalophus wollebaeki) rookeries as a result of variance in ecosystem metrics and population abundance. We used skull measures related to individual size and aggressiveness. We analyzed 19 linear measures for size and 15 for aggressiveness taken on 49 adult male skulls of GSL collected in four bioregions of the archipelago. Nine skull measures had a significant effect on individual clustering into bioregions (P < 0.001). The most discriminating measures were snout length, supraorbital process width, nasal length, and canine width. We found a significant relationship between skull grouping patterns and chlorophyll-α levels (proxy marine productivity and body growth) and GSL population abundance (proxy of agonistic behavior) of each bioregion, as well as with the interaction between both variables (P < 0.001). Our results suggest significant regional differences in GSL skull morphometry, which could be associated with resource availability and level of male intrasexual competition in the archipelago. This information is important for understanding the life history of this species.