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Matched sets of gillnets of different mesh-sizes were used to evaluate the degree to which contiguous and connected flooded forest and floating meadow habitats are characterized by distinct fish faunas during the flooding season in the Peruvian Amazon. For fishes between 38–740 mm standard length (LS) (the size range captured by the gear), an overriding pattern of faunal similarity emerged between these two habitats. The mean species richness, diversity, abundance, fish mass, mean and maximum LS, and maximum mass did not differ significantly between flooded forest and floating meadows. Species abundances followed a log-normal distribution in which three species accounted for 60–70% of the total abundance in each habitat. Despite these similarities, multivariate analyses demonstrated subtle differences in species composition between flooded forest and adjacent floating macrophytes. In addition, the absolute number of species was higher in flooded forest, reflecting a higher percentage of rare species. The day–night species turnover was found to be greater in flooded forests than floating meadows. Further, nocturnal samples had higher abundances and greater species richness than diurnal samples in both habitats. Differences in habitat structural complexity between flooded forest and floating meadows may result in a higher abundance and species richness of day-active species in floating meadows.