The whale shark Rhincodon typus (Smith, 1828) is a filter-feeding species that feeds on zooplankton. There are whale shark aggregation sites in the Gulf of California, Bahia de La Paz in Baja California Sur, and Bahía de Los Angeles in Baja California. Whale shark ecotourism is an important and economically profitable activity for the coastal communities surrounding their habitat areas. Fatty acid (FA) profiles, including arachidonic acid (ARA), docosahexaenoic acid (DHA), and eicosapentaenoic acid (EPA), are used as trophic tracers in marine food webs because they are essential for marine fish and provide information on the nutritional quality of zooplankton. In the present study, we analyzed the FA profile of zooplankton to trace them in the stomach contents, blood, liver, and muscle of stranded male whale sharks and the subdermal tissue of live whale sharks. Total lipids were extracted to calculate the energy density. Then lipids were methylated to obtain FA methyl esters (FAMEs) and analyzed in a gas chromatograph with a flame ionization detector. Permutational multivariate analysis of variance was applied to compare FA profiles. Zooplankton of both aggregation sites had 70% similarity in their FA profiles. The FA profile found in the liver of whale sharks was similar to that of zooplankton in both aggregation sites (DHA>EPA>ARA). However, muscle and subdermal tissue had FA profiles significantly different from zooplankton, and there was preferential ARA assimilation in the subdermal tissue of stranded and live whale sharks. Therefore, FA profiles reflected just 50-60% of the diet, suggesting that whale shark tissues retain FA according to their metabolic requirements or that surficial zooplankton do not provide ARA detected in subdermal tissue. Future studies should consider night sampling and FA analysis of demersal zooplankton in each aggregation site.