The potential effect of forest type on the structuring of animal communities in western Amazonia remains poorly understood. In this study, we tested the hypothesis that amphibian species richness, composition and abundance differ across forest types in the lowland rain forest of south-eastern Peru. By using 320 individual transects, we compared the amphibian assemblages across four major forest types (floodplain, terra firme, bamboo and palm swamp) at each of four sites separated by 3.5-105 km. We identified 1967 individuals of 65 species in 11 families and found that a large proportion of the amphibian diversity in this region is attributed to habitat-related beta diversity. Overall, we found that forest type is more important than site in predicting both species composition and abundance. We also found that, when analyses are conducted separately for each forest type and include species abundance data, similarity between assemblages decreases with increasing geographic distance. In contrast to studies that considered species presence/absence but ignored species abundances, our results highlight the importance of including abundance data in the assessment of animal diversity patterns in western Amazonia. We conclude that evaluating community structure across forest types can improve our understanding of diversity patterns in this region. Copyright © 2010 Cambridge University Press.