Widespread conversion of deciduous forests to agriculture in the midwestern United States has resulted in landscapes whose remaining native habitats are highly fragmented, with well-documented consequences for wildlife community structure. We analyzed trap data for 5 forest rodent species from 525 sites in 35 study landscapes throughout the upper Wabash River basin, which is dominated by agricultural use and drains >20% of Indiana. We used a recently developed likelihood approach and multi-model inference to obtain unbiased estimates of occurrence probabilities for a species when detection rates are <1, and we used hierarchical generalized linear modeling to evaluate random effects associated with nested data structure. Inclusion of a spatial autocovariate term had important effects on model selection results for 4 of 5 species and improved fit of models. Eastern chipmunks (Tamias striatus), although previously described as sensitive to fragmentation, were nearly ubiquitous in our study region and had greater occupancy rates in smaller woodlots. Fox squirrels (Sciurus niger) are well adapted to patchy landscapes, and their occupancy rates actually increased with patch isolation. Gray squirrels (S. carolinensis) are adversely affected by forest fragmentation; we observed a threshold decline in occupancy rates beyond ∼15 km from the Wabash River, which harbors the only source of contiguous habitat within the entire river basin. Red squirrels (Tamiasciurus hudsonicus) exhibited greater abundance in sites without gray squirrels. Moreover, their occupancy rates were positively related to habitat and landscapes considered suboptimal (e.g., lower basal area of hard-mast bearing trees, more isolated patches); this was further evidence for negative effects of gray squirrels on red squirrel populations. White-footed mice (Peromyscus leucopus) were nearly ubiquitous; although occurrence rates in less forested landscapes increased with distance from edge and greater volume of woody debris.