This study evaluated the trophic ecology of two annual fish species, Austrofundulus guajira and Rachovia hummelincki, in temporary ponds in the department of La Guajira, Colombia. Sampling was carried out in two ponds in the municipality of Maicao between November 2018 and January 2019, using trawls and atarray nets for fish collection. The fish diet was characterized by analysis of gut content, and frequency of occurrence, volumetric and relative importance indices were used for comparison. Additionally, the trophic position and omnivory index were estimated, and trophic niche breadth was calculed using the Levins index standardized by Hurlbert (Bj). The results show that R. hummelincki is an insectivorous and zooplanktophagous species, and its breadth of trophic niches suggests that it is a specialist. On the other hand, A. guajira was characterized as herbivorous, insectivorous, zooplanktophagous, piscivorous and opportunistic, and is considered a generalist species with a Levins index of 0.66. Limited overlap of the trophic niche was seen between the two species, suggesting partitioning of the trophic niche and differentiation of consumed resources to decrease competition. In addition, marked differences were found in the diets of the two species, even though both are considered omnivores and have different trophic positions. This study contributes to knowledge of the trophic ecology of annual fish in temporary pools and highlights the importance of trophic niche partitioning for species co-existence in vulnerable and ephemeral ecosystems such as temporary ponds. The results may also be relevant for the conservation of biodiversity in aquatic environments and for the decision making in natural resources.