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In Colima, Mexico, we conducted 8-night mark–recapture grid studies of southern pygmy mice ( Baiomys musculus (Merriam, 1892)) in January 2003–2007 in dry deciduous and tropical moist forests. For 40 000 trap-nights, 436 individuals were captured 764 times (comprising 18.6% of small mammals). The male:female ratio was 1:1.37, 82.9% were adults, 51.4% of females were pregnant or lactating, and coastal animals, on average, were heavier than those inland. Females moved farther than males. Baiomys was on 17 of 25 grids (densities 1.82–106.24 individuals/ha). Moon illumination did not affect capture or recapture probabilities, but trap-night did (overall, probability increased 1.66%/night). Grids with Baiomys had less bare ground and a more open canopy. Capture sites had more grass, less dead wood and bare ground, a more open and lower canopy, and greater distance to trees. Logistic regression indicated coastal capture sites had more forbs, grasses, and woody plants, and thicker vegetation at 1 m height with trees being relatively distant. Variables differed somewhat for northern sites, and the equation for all grids included 10 of 14 environmental variables. Baiomys frequented edge of an unimproved road traversing one grid. Baiomys musculus, widespread in Colima, exhibited preference for habitats with relatively dense ground cover and at least a partially open canopy.