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This scientific study analyzes the biodiversity of birds and mammals in flooded ecosystems of Loreto, Peru, with the objective of understanding their ecological patterns and their relationship with floristic richness. Systematic censuses were applied at different times of the year and forest strata, complemented with statistical analyses such as the Margalef index, which allowed the identification of 757 species with varying degrees of abundance and ecological specialization. The research revealed significant associations between trophic groups (frugivores, insectivores, omnivores) and vegetation types, as well as the differentiated use of microhabitats and altitudes by key species, reproductive behavior dynamics, local migration patterns and interspecific coexistence, which provides a more complete view of the ecological functioning of the system. Floristic richness was positively correlated with faunal diversity, highlighting indicator species that could be used in ecological monitoring and adaptive conservation. The study emphasizes the need to incorporate multiscale criteria in the design of conservation and management strategies.