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Resource competition with commercial fisheries and changes in prey availability related to El Niño Southern Oscillation (ENSO) events have adversely affected guanay cormorant (GC, Phalacrocorax bougainvilli aka Leucocarbo bougainvilliorum) and Peruvian pelican (PP, Pelecanus thagus) populations within the Humboldt Current marine ecosystem along coastal Peru. Ecosystem effects from environmental and anthropogenic impacts can result in decreased population sizes and declines in immune function, fecundity, and overall species' health. We measured circulating fat-soluble vitamins A and E, four carotenoids, five trace minerals [Cu, Fe, Mn, Pb, Zn], 13 free fatty acids, and 31 amino acids in GC and PP from Punta San Juan, Peru. We found significant differences in nutrient status between species, sexes, and body weights. There were 82 GC and 34 PP sampled in total: body weights were significantly (p < 0.001) higher in males (2.20 ± 0.15, 6.05 ± 0.47 kg) than females (1.96 ± 0.14, 4.88 ± 0.25) of both species (GC and PP, respectively). Pelicans displayed lower vitamin A concentrations (0.48 ± 0.07 µg/ml) than GC (0.67 ± 0.15 µg/ml) but higher total carotenoids (10.24 ± 2.55 and 5.70 ± 1.87 µg/ml; p < 0.05); vitamin E concentrations did not differ between species (GC 7.74 ± 2.87, PP 8.45 ± 2.16 µg/ml). Within minerals, copper (352.53 ± 206.17, 214.97 ± 25.33 ng/ml) and manganese (11.13 ± 3.85, 8.75 ± 4.36 ng/ml) concentrations were higher and zinc (1.69 ± 0.30, 2.15 ± 0.30 µg/ml) was lower in GC (n = 31) than PP (n = 34), respectively, p < 0.05). Fatty acid (FA) profiles differed between species in that GC had lower levels of circulating EPA (p = 0.026) and DHA (p < 0.001), resulting in lower n-3/n-6 ratios for GC (2.57 ± 0.91) compared with PP (4.69 ± 0.95) (p < 0.001). PP had higher levels of palmitic acid (p < 0.0001). No differences in FA were found between sexes. On the contrary, circulating amino acid (AA) profiles were broadly similar between species for essential AAs, but differed widely for several of the non-essential AAs, suggesting different primary prey items consumed by species and/or sexes. These results provide baseline information on circulating nutrient concentrations and may be useful for comparison of different foraging strategies/prey base use in these sympatric species, as well as for the evaluation of temporospatial variations that may result from anthropogenic causes, including changes in ENSO events. Knowing the diets of these species in the wild helps in providing them with better diets in captivity that could promote health and fecundity.