Deep-sea fishes substantially contribute to vertical carbon transfer through diel vertical migration and support nutrient cycling through deep-ocean food webs, yet survey gear biases frequently mask true patterns of abundance and taxonomic composition. Relationships between species traits and capture probability remain poorly defined, complicating cross-gear comparisons and inference. Accurate evaluations of species compositions and gear-specific selectivity are critical for ecosystem-based management, informing stock assessments, habitat protection, and conservation priorities. By correcting gear-related biases and improving biodiversity estimates, researchers and managers can better interpret ecological baselines, assess species vulnerability, and monitor population trends. This research developed species-level catchability indices by directly comparing taxa captured by the Irish Herring Trawl (IHT) and Multiple Opening/Closing Net and Environmental Sensing System [MOC10) across overlapping depth strata. Paired sampling targeted the mesopelagic (0-1000 m) and upper bathypelagic (0-1500 m) zones in the Gulf, with standardization by depth and hydrographic conditions to account for Loop Current variability. Individual specimens were measured for standard length, body width, and body depth and were scored for locomotory mode, fin-ray morphology, and dentition. Generalized linear mixed models related differences in catch-per-unit-effort (CPUE) to net type and species traits to estimate retention probabilities at both species and trait levels. Derived retention probabilities generated calibration factors that adjusted CPUE estimates for taxa sampled by both gears. Quantifying catch efficiency and species-specific retention across gear configurations and applying those probabilities to future MOC10 and IHT surveys enable calibration and direct comparison of survey results. These bias-corrected indices can inform sustainable fisheries management, improved standardization of ecosystem and carbon-flux models, and guide adaptive conservation strategies in the aftermath of large anthropogenic disturbances such as oil spills.