Food partitioning among coexisting species is often considered advantageous to minimize niche overlap and avoid inter-specific competition. Congeneric fish species such as the mullets Mugil curema and Mugil liza, which co-occur across marine and estuarine habitats, are good models to evaluate resource use and niche overlap or partitioning. We used stomach contents (SCA) and stable isotope analysis (SIA) to assess potential trophic shifts and changes in niche overlap associated with the mullets transitioning from marine to estuarine habitats. SIA included different fractions of organic matter in suspension and in the sediment to estimate the contribution of micro, nano and pico-organisms to the mullets’ diets. We hypothesized higher resource partitioning in the less resource-diverse system (marine surf-zone) than in the more diverse one (estuary). SCA showed diet differences between M. curema and M. liza according to the habitat. They showed distinct diets in the marine area (P < 0.001), but similar diets in the estuary (P = 0.226). A lower niche breadth was observed for both species in the marine area (M. curema = 0.03, M. liza = 0.06) compared with the estuary (M. curema = 0.14, M. liza = 0.16). Isotopic niches of both species were higher in the estuary (64.7%) compared with the marine area (0.7%). These findings corroborated our hypothesis of higher food partitioning in the marine surf-zone. We also demonstrated using SIA the shift from planktonic to benthic feeding following the recruitment of the mullets from the surf-zone into the estuary.