Food partitioning among coexisting species in different habitats remains an important research topic in trophic ecology. In this work, we combined carbon and nitrogen stable isotope ratios and stomach content analyses to investigate differences in diet and niche overlap of two congeneric juvenile mullet species (Mugil curema and Mugil liza) coexisting in a marine surf-zone and an estuarine zone in southern Brazil (29oS). These habitats have contrasting levels of food availability, especially in terms of prey diversity, with higher microalgae diversity in the estuary than in the marine surf-zone. In these contrasting conditions, we predicted that both mullet species will have (a) higher niche overlap and smaller niche breadth at the marine surf-zone due to the common exploration of highly abundant surf-zone diatoms and (b) lower niche overlap and higher niche breadth inside the estuary due to selective feeding on more diverse food resources. Isotope niche areas (measured as standard ellipse areas) were higher in the estuary (6.10 and 6.18) than in the marine surf-zone (3.68 and 3.37) for both M. curema and M. liza, respectively. We observed an overlap of 52% in isotopic niches of both species in the marine surf-zone and none in the estuary. We also found contrasting patterns in the diet composition between species according to the habitat. At the marine surfzone, diatoms of the classes Bacillariophyceae and Coscinodiscophyceae dominated (> 99%) the food content of both mullet species. In contrast, green algae, cyanobacteria, dinoflagellates and flagellates comprised the diet of both species in the estuary. These results could be explained by spatial differences in food availability (especially regarding diversity of microalgae) between both habitats. At the marine site, both species explored the most abundant microalgae available (mostly the surf-zone diatom Asterionellopsis cf. guyunusae and fragments of Coscinodiscus), whereas in the estuary both species shifted their diets to explore the greater diversity of microalgae resources. Overall, our findings revealed that niche partitioning theory could not fully predict changes in breadth and overlap of food niches of estuarine dependent fish species with complex life cycles encompassing marine to estuarine systems with contrasting food availabilities.