Bulk tissue stable isotope analysis (i.e. analysis of δ15N values; BSIA hereafter) has been widely applied to understand the trophic ecology of sea turtles and the nutrient dynamics of marine systems they utilize. However, interpretation of δ15N values from bulk tissue analysis can be confounded by nutrient dynamics and their effect on nitrate δ15N values. Amino acid compound specific nitrogen isotope analysis (AA-CSIA) may provide more accurate information on the trophic position of an organism by accounting for differences in δ15N values at the base of the food web. Applied AA-CSIA has the potential to add value to trophic ecology studies, specifically, to studies that include wide ranging animals like sea turtles that occupy multiple ocean regions and habitats throughout different life stages. However, AA-CSIA critical parameters remained unresolved for many taxa. The East Pacific green turtle (Chelonia mydas; hereafter referred to as the green turtle) occupies foraging grounds throughout the eastern Pacific Ocean. Green turtle foraging habitats vary in their structure and exposure to anthropogenic impacts and bulk tissue δ15N values have been variable in green turtle foraging aggregations across their East Pacific range, making it challenging to determine whether these differences are driven by divergent trophic interactions or variability in the nutrient dynamics (i.e. organic nitrogen) specific to foraging habitats. The two parts of this thesis were to first establish green turtle-specific parameters for AA-CSIA in a controlled study and second to use AA-CSIA parameters to calculate green turtle trophic position in the distinct habitats of San Diego Bay, California and Laguna San Ignacio, Mexico. The controlled study established amino acid δ15N values for green turtle skin and plasma and green turtle trophic discrimination factors of 3.9‰ and 6.5‰ for skin and plasma respectively. AA-CSIA trophic position calculations of 3.0 for green turtles in San Diego Bay and 2.1 for green turtles in Laguna San Ignacio reveal the influence of habitat structure on trophic interactions across their range. This thesis represents the first determination of critical AA-CSIA parameters for a marine reptile and a field study to support future application of AA-CSIA to study sea turtle ecology.