Rocio is a small genus of Neotropical freshwater fishes that is distributed in Atlantic drainages of northern Middle America. Two species of Rocio, R. spinosissima and R. octofasciata, exhibit sympatry in the Río Dulce basin in eastern Guatemala. Rocio spinosissima is endemic to the Río Dulce basin, while R. octofasciata has a larger geographic range that includes this area. Our goal was to explore the ecological and morphological variation shown by these two closely related species and determine their differences. A combination of field work, analysis of museum specimens, and ecological niche modelling helped to better understand the differences in habitat and environmental characteristics, along with the body shape variation. Local‐scale environmental data suggest that both species inhabit lentic environments, with R. spinosissima using narrower and low canopy‐covered habitats and R. octofasciata inhabiting areas with a larger range of environmental characteristics. Ecological Niche Models indicated that land cover, soil, precipitation, and temperature largely define the distribution of both species. Body shape differs between species, with R. spinosissima exhibiting a rounder and deeper body while R. octofasciata is more elongated. Specimens of R. octofasciata across its distribution also show variation in head shape, mouth position, fin, and caudal peduncle characteristics, possibly as a response to trophic strategies that reduce competition. Similarities in their environments and morphologies allow us to identify broadly overlapping niches in the two species of Rocio, while the fine scale differences documented between species will have conservation implications for the endemic R. spinosissima.