Total mercury (Hg) levels were determined in the tissues of ten taxa of pelagic fishes, with a special emphasis on apex predators (large vertebrates). Highest Hg levels were observed in blue marlin (Makaira nigricans), carcharhinid sharks (Genus Carcharhinus) and little tunny (Euthynnus alletteratus), ranging from 1.08 to 10.52 ppm. Moderate to low concentrations (<1.0 ppm) were observed in blackfin tuna (Thunnus atlanticus), cobia (Rachycentron canadum), dolphinfish (Coryphaena hippurus), greater amberjack (Seriola dumerili), king mackerel (Scomberomorus cavalla), wahoo (Acanthocybium solandri) and yellowfin tuna (Thunnus albacares). For the majority of species examined, Hg level did not vary significantly between locations (Texas and Louisiana) and years (2002 and 2003). The relationship between Hg level and fish size/weight was also explored and six taxa (blackfin tuna, carcharhinid sharks, dolphinfish, king mackerel, wahoo, yellowfin tuna) showed significant positive relationships between Hg level and body size and/or weight. Natural dietary tracers, stable isotopes (15N, 13C) and fatty acids were used to evaluate the relationship between Hg and trophic position and the relationship between Hg and dietary history. Stable nitrogen isotope analysis showed that Hg levels in fish tissues were positively associated with trophic position. Based on the 13C and 15N values of pelagic consumers examined in this study, three natural groups were identified with cluster analysis, and the same groupings were detected based on fatty acid profiles. This not only confirmed the existence of these natural groupings, but also indicated that the distinguishing factors for the grouping was likely connected with the dietary history of these fishes. The classification tree based on the fatty acid profiles of pelagic fishes readily separated fishes from different regions, suggesting that diets of pelagic taxa within the same region are similar or these consumers share a common source of organic matter in their food web. Findings from this study complement other Hg investigations conducted in the Gulf and also furthered our understanding of the link between feeding ecology and Hg accumulation. Moreover, the combined use of stable isotope and fatty acid techniques provided new insights on the dietary history of pelagic fishes in the Gulf of Mexico.