<p>Amazonia harbors the greatest diversity of freshwater species worldwide and several endemism areas. However, anthropogenic activities are rapidly transforming its landscapes. Odonata are insects that respond to environmental changes in aquatic and terrestrial ecosystems. Their flight performance and thermoregulation abilities influence their permanence in habitats. This study analyzed how stream condition and biogeographic province in Amazonia determine the functional structure of Odonata assemblages and, consequently, their habitat specialization. We also assessed whether the Odonata species’ specialization response to environmental degradation depends on the suborder and the biogeographic province. We sampled adult Odonata assemblages in streams distributed in two different biogeographic provinces of Amazonia and measured the stream condition using the Habitat Integrity Index. We calculated the components of functional structure (richness, evenness, divergence, and originality) and functional specialization of assemblages in each biogeographical province. We found that components of functional structure respond differently to habitat integrity and biogeographic province. Functional specialization of assemblages is influenced by habitat integrity, functional divergence, and originality. This implies that only assessing the different components of functional diversity would give us a more comprehensible understanding of the assemblages’ response. Moreover, the response of species specialization to habitat integrity varies according to Odonata suborder.</p>