In aquatic systems, macrophytes play an important role in habitat structuring and can be relevant for the establishment and/or mobility of the organisms and might thus influence species composition. This study evaluates the influence of the structural complexity of aquatic plants on the community composition of Ostracoda in the upper Paraná River floodplain. We tested the hypothesis that non-swimming and small-sized species have a higher association with more complex plants by a threshold indicator taxa analysis. Some small and non-swimming ostracod species had a significant affinity for macrophytes with higher complexity, especially Eichhornia crassipes. However, most species did not show an association with the structure of aquatic macrophytes, and there was only a slightly distinction among the communities of different plants. The results show that structural complexity is in some cases an important determining factor for the community composition of Ostracoda, but other factors may interact with and even override the effects of complexity. It can thus be concluded that the relation between habitat complexity and the Ostracoda community composition is complex and not always responds to general predictions.