Amazonian lowland rain forests are complex three‐dimensional formations consisting of a variety of arboreal and terrestrial habitats. The small mammal faunas, particularly of arboreal habitats, are poorly studied, and field research generally has been limited to a few faunal inventories. We sampled the terrestrial and arboreal small mammal fauna in two floodplain forest study zones at Reserva Cuzco Amazonico, southeastern Peru, by removal trapping for 12 consecutive days in dry (June‐July 1989) and rainy seasons (January‐February 1990). Nineteen taxa of marsupials and rodents were captured. Small mammals were more abundant in the rainy season than in the dry season, but the relative proportions of the 11 most abundant species remained stable between seasons and study zones. Most species showed no decline in capture rates through the 12‐day period, indicating that either population densities were high or animals were quite mobile. The small mammal fauna exhibited strong vertical stratification; among the 11 most abundant species, four exhibited strong biases toward terrestrial and five toward above‐ground captures. The distinct arboreal small mammal community is grossly underrepresented if traps are placed only at gro