To investigate the potential long-term consequences of environmental warming in subtropical systems, we compare the trophic structure of shallow lakes in tropical and subtropical regions. In total, 25 meso-eutrophic lakes with piscivorous fish were sampled during summer along a latitudinal gradient in South America. The fish catch per unit of effort and the omnivorous fish to zooplankton biomass ratios were significantly lower in the tropical lakes. Despite the lower fish biomass, no significant difference was found in zooplankton or phytoplankton communities or in the zooplankton to phytoplankton biomass ratio between the two sets of lakes. Nevertheless, regression models based on the combined dataset show higher cyanobacteria and total phytoplankton biomass at lower zooplankton to phytoplankton biomass ratio and higher omnivorous fish to zooplankton biomass ratio. Cyanobacteria biomass was dominated by non bloom-forming taxa and was inversely related to the biomass of calanoid copepods suggesting that these herbivores may play an important role in controlling edible cyanobacteria in warm shallow lakes. Overall, our results, however, suggest that warming will have relatively minor impacts on the pelagic trophic structure of shallow subtropical lakes supporting the idea of weaker trophic cascades in warm (sub)tropical lakes in comparison to temperate ones.