Species coexistence depends on how organisms utilize their environmental resources, namely trophic niche partitioning. The comparative study of interspecific trophic niches is helpful for understanding the coexistence mechanism of sympatric species. Fatty acid profiles reflect the feeding information of organisms obtaining a relative long time scale, and play an important role of revealing the trophic niche partitioning among species. There are eight pelagic shark species inhabiting in the tropical Eastern Pacific, including blue shark (Prionace glauca), silky shark (Carcharhinus falciformis), oceanic whitetip shark (C. longimanus), bigeye thresher shark (Alopias superciliosus), pelagic thresher shark (A. pelagicus), shortfin mako shark (Isurus oxyrinchus), scalloped hammerhead shark (Sphyrna lewini), and smooth hammerhead shark (S. zygaena). To study the differences of their feeding habits, nutritional relationship and trophic niche partitioning, the fatty acid profiles o f shark muscle tissues were analyzed. Results showed that shortfin mako shark occupied the highest trophic level while blue shark occupied the lowest one. The trophic niche overlap of bigeye thresher shark, pelagic thresher shark and shortfin mako shark indicated their intense prey competition and the spatial segregation compared with other shark species were also detected. Bigeye thresher shark showed the most niche similarity to pelagic thresher shark, indicating they may compete for the same resources. Blue shark and silky shark occupied the largest trophic niche area indicating their strong environmental plasticity. Shortfin mako shark and scalloped hammerhead shark occupied the smallest trophic niche area, which may imply the specialization of their feeding habits and this was proved by their relatively high trophic levels. This study demonstrated the potential application of fatty acid profiles in shark feeding ecology studies, especially in the fields of their trophic niche partitioning, allocation patterns and coexistence mechanism.