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Fish predation and habitat structure provided by aquatic plants influence wetland macroinvertebrates. However, the patterns of macroinvertebrate distribution (including their functional structure) in relation to fish occurrence and plant habitats comprised by differently shaped macrophytes remain challenging to predict in many wetland systems, and are especially little studied in the Neotropics. We assessed the effects of fish presence and aquatic plant habitat types with different levels of structural complexity (Sphagnumbogs: 'high complexity'; Peruvian watergrass: 'low complexity') on the taxonomic and functional structures of macroinvertebrate assemblages in the southern Brazilian highland wetlands. We tested the expectations that macroinvertebrate assemblages have: (1) a lower richness and abundance, and are comprised by taxa with traits related to less prey vulnerability in the presence of fishes; (2) a higher richness and abundance in plant habitats with higher complexity, and distinct taxonomic and functional compositions among habitats. Six wetlands of similar hydroperiods presenting both habitat types and differing according to fish presence (three wetlands contained predatory fish species; the other three were fishless) were seasonally sampled in 2012 and 2013. Macroinvertebrate assemblages changed only according to the fish presence. Richness and abundance were higher in fishless wetlands, and the effect of fish presence on macro- invertebrate taxonomic and trait compositions was also related to each wetland, suggesting varying effects of fish species. Our results suggest that macroinvertebrate assemblages are primarily structured by fish presence rather than plant habitat types in highland wetlands in southern Brazil, and that the influence of plant habitats possibly co-varies with other local environmental factors.