A major goal of ecological research is the ability to accurately model food web dynamics in order to increase the accuracy of ecosystem models. Before accurate food web models can be constructed, information regarding trophic relationships among functional groups, estimates of trophic position, and factors influencing trophic structure using stomach content analysis (SCA) and stable isotope analysis (SIA) must be completed. Currently, several comprehensive data sets using SCA to describe trophic structure of micronketon in the deep-pelagic Gulf of Mexico (GoM) exist but data derived from SIA are less common. Bulk δ13C and δ15N data from vertically migrating (25 species), and non-migrating taxa (25 species), representing a range of feeding strategies, depth distributions, and putative trophic levels were selected in order to describe trophic variability within the GoM micronekton assemblage. The δ13C values of micronekton varied among species, ranging from -22.73‰ to -16.35‰ suggesting micronekton are supported by phytoplankton-based food webs throughout the water column. Micronekton δ15N values ranged from 1.85‰ to 10.97‰ encompassing ~3 trophic levels. Body size and depth of occurrence were both positively correlated with δ15N suggesting both factors significantly shape trophic structure in GoM micronekton assemblages. Elevated δ15N values in many non-migratory taxa were higher than expected based on SCA suggesting increased reliance on food webs with 15N enriched baselines at lower meso- and bathypelagic depths. This project provides novel SIA data that can be used to inform GoM ecosystem models and will provide insight into the structure of the northern GoM deep-pelagic ecosystem.