Many Caribbean nations lack information on the ecology and biology of marine species, which are essential for food security and livelihoods in the region. This study aimed to advance the knowledge of two commercially important fish species, lane snapper (Lutjanus synagris) and white grunt (Haemulon plumierii), using cost-efficient techniques. Specifically, geometric morphometrics was used to assess the presence of ecomorphological groups (characterized by body shape variation associated with local environmental variables) in the Honduran Caribbean continental platform. Photographs of 104 lane snapper and 99 white grunt adult individuals were taken and digitalized with 12 landmarks. Subsequently body shape patterns were related to environmental variables using Distance-based linear models and Partial Least Squares. Results enabled the identification of ecomorphological groups or fish stocks in the study region associated with the environmental conditions of each site. Distance to river mouth and Chlorophyll a, both indicators of land-based stressors, appeared as the primary driving force of body shape differentiation in the species. These results are key for the development of informed reef fisheries management policies in the Caribbean region.