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Habitat complexity can substantially alter trophic relationships, such as competitive and predatory interactions, between fish species. This study aimed to evaluate how trophic interactions between congeneric fish species (Serrapinnus calliurus, S. heterodon and S. notomelas) are affected by habitat complexity provided by macrophytes. The following predictions were tested: (1) the composition of the diets of congeneric fish species differs between high- and low-complexity habitats and between habitats of the same category; (2) species show higher trophic niche breadth in sites with greater habitat complexity; and (3) trophic niche overlap between congeneric species pairs is low in macrophyte stands because of greater food availability. Sampling was conducted between November 2011 and July 2012 in five floodplain lakes of the Baía River, a tributary of the upper Paraná River. The degree of habitat complexity was categorised as high (with macrophytes) or low (without macrophytes). The stomach contents of the three species sampled from sites of high- or low-complexity habitat were analysed. Diet variation depended on habitat complexity. The median trophic niche breadth of the three congeneric species was low, but their diets showed higher variability in sites of high-complexity habitat. Significant differences in trophic niche overlap were observed in two species pairs when comparing sites of high- and low-complexity habitat. Habitat complexity directly affected trophic interactions between the fish species, which may favour their coexistence through trophic niche segregation. Our study emphasises the importance of habitat complexity in mediating trophic interactions between congeneric species and clarifies the coexistence of ecologically similar fish species. [ABSTRACT FROM AUTHOR]