Aquatic macrophytes have a key role in aquatic ecosystems because they can structure biotic communities by offering habitat for many aquatic organisms, especially periphytic algae. The aim of this study was to evaluate the periphytic algal structure (taxonomic diversity and functional traits) in two macrophytes with different architectures (Nymphaea L. and Cabomba Aubl.). We tested the hypothesis that architectures of the Nymphaea and Cabomba affect in a different way the periphytic algae community, increasing taxa richness and density in more complex substrate (Cabomba), and that the taxa composition, life form and adherence form are different between both types of macrophyte. In addition, we tested whether there is higher algae density without a fixed structure on complex substrate. The study was conducted in Caxiuana National Forest, one of the largest protected areas in the Para state, Eastern Amazon. The samplings were made in blocks with two levels (Nymphaea and Cabomba) under the same abiotic conditions. Our results showed that there was a significant difference in taxa richness and density between macrophytes, with higher values in Cabomba. We found more exclusive species in more complex substrate (70, Cabomba), than less complex substrate (19, Nymphaea). Furthermore, species composition, life form and adherence form also showed differences between macrophytes, with higher algae density without a fixed structure on Cabomba. These results indicated that when the source of algal propagules is the same (mixed bank of macrophytes), the habitat complexity tightly influenced the diversity of periphytic algae community.