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The role of native trees, Fremont cottonwood (Populus fremontii) and Goodding willow (Salix gooddingii), in structuring the riparian small mammal assemblage on rivers in the American desert southwest is unclear. It is unknown, for example, whether these trees directly or indirectly provide the food or shelter necessary for the presence of any species. Because of the rapid and widespread decline of gallery forest, due in part to river regulation, the retention of remnant stands and replacement of lost stands are major regional conservation issues. To elucidate small mammal-forest linkages, we compared patterns of macrohabitat use among terrestrial small mammals at two rehabilitated and one unmanipulated alluvial floodplain site along the highly regulated lower Colorado River. We also compared current patterns to the Colorado River faunal associations Joseph Grinnell documented in 1910, prior to significant flow regulation. We used grid-based, capture-mark-recapture techniques at two revegetation sites, each a mosaic of six distinct macrohabitats, including planted cottonwood/willow, to associate species with specific macrohabitats. We also trapped a ’reference’ grid containing naturally regenerating cottonwood and willow at a site on the lower Bill Williams River floodplain. Despite very poor development of cottonwood plantings at one of the revegetated sites, each supported at least nine species and harbored all seven species that Grinnell associated with areas flooded nearly every year. The set of species Grinnell associated with cottonwood/willow stands (Peromyscus maniculatus, Reithrodontomys megalotis, and Sigmodon arizonae) was trapped at both revegetation sites but entirely absent at the reference site. The Bill Williams site may be inaccessible to Sigmodon, but the absence of the other two species is probably a consequence of differences in floodplain structure and functioning among the study sites as well as between the Bill Williams site and historic Colorado River riparian areas. Our data suggest the richness of the native lower Colorado River riparian small mammal assemblage is unrelated to the presence or absence of cottonwood/willow trees, but does depend in part upon the presence or absence of dense herbaceous vegetation. Resource managers attempting to rehabilitate degraded desert riverine ecosystems need to consider understory as well as overstory plant species in revegetation efforts. Copyright (C) 1999 John Wiley & Sons, Ltd.