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We describe the nonvolant mammal fauna of the Rio Juruá of the western Amazon of Brazil, based on collections made during a year-long survey of the river. We, along with our colleagues Drs. Claude Gascon and Carlos Peres, designed the field project to examine the effects of the river on the differentiation among terrestrial vertebrates (mammals, birds, and amphibians and reptiles) at both the community and population levels. This monograph examines only the patterns of geographic variation and community structure of the small-bodied mammals. Species inventories were made at 16 primary trapping localities divided into eight pairs of cross-river sites, with two pairs in each of four regions from near the mouth to the headwaters of the Rio Juruá. A total of 81 species of nonvolant mammals were obtained, including nine new to science. Four of these are described herein; the others have been described elsewhere. We used a standardized trapping protocol to assess community structure at each of the 16 localities that included terrestrial and canopy trap stations in floodplain (várzea) and upland (terra firme) forest formations. Supplemental trapping was done in secondary habitats at all sites. We describe these sites, the trap effort expended, and the placement of trap stations relative to local habitats. We also describe each species of marsupial, sciurid rodent, murid rodent, and echimyid rodent encountered; comment on their systematics; and summarize aspects of habitat use, life history, geographic distribution, and geographic differentiation based on morphological and molecular traits. We examine patterns of differentiation in the mitochondrial cytochrome-b gene for samples of 41 of the 45 species of marsupials and rodents obtained within the Rio Juruá Basin, and discuss these patterns from the perspective of the entire Amazon and, in some cases, the Mata Atlântica of coastal Brazil. We also examine patterns of community organization within the Rio Juruá basin and throughout Amazonia, drawing attention to the geographic distribution of what appear to be major faunal units that are independent of habitat differences. Finally, we use principles of phylogeography to analyze patterns of geographic differentiation among the nonvolant mammals with regard to the Riverine Barrier Hypothesis. We show that, while there are few examples of taxa for which the Rio Juruá is apparently a barrier, most taxa either are largely undifferentiated throughout the basin or are sharply divided into reciprocally monophyletic mtDNA haplotype clades separable into upriver and downriver units. We argue that the concordance in the geographic placement of clade boundaries suggests a common history; moreover, both the age of these clades and their geographic position in relation to underlying geological features suggest that landform evolution has been an important, but underappreciated component of diversification within western Amazonia.