Habitat loss and fragmentation are likely to affect individual condition as they usually alter the quality of habitat. However, responses of individuals of different species to these processes may be subtle and difficult to detect, despite that such responses may reveal interesting and diverse strategies of persistence of species in fragmented landscapes. Here, we used model selection to 1) compare the body condition (Scaled Mass Index) of 2 Neotropical marsupials (Didelphis aurita and Philander frenatus) from 6 continuous forest sites and 25 forest fragments, and 2) determine whether local habitat structure and landscape and temporal factors affect body condition in forest fragments. Body condition of both species was lower in forest fragments compared to continuous forest sites, but only in the super-humid season for D. aurita and in the humid season for P. frenatus. When only forest fragments were compared, body condition of D. aurita was higher in the humid season, in sites with fewer Cecropia trees and water courses, lower percent forest cover, and surrounded by a mixed matrix (plantation and cattle ranching), or located in small rural properties. Body condition of P. frenatus was slightly higher in the super-humid season, in sites surrounded by a mixed matrix, with fewer Cecropia trees and water courses, more lianas, and greater percent forest cover. Our results revealed negative effects of habitat loss and fragmentation on both species, but also different responses of each species to local extrinsic environmental factors. We suggest that body condition should not be used as a direct indicator of animal fitness or habitat quality. Nonetheless, body condition may still reveal subtle and previously undetected responses of species to habitat disturbance and fragmentation.