Understanding the habitat preferences of native and non-native species may offer valuable insights into the mechanisms favouring invasion of disturbed habitats. This study investigated the determinants of trap-site detection probability of three native (Maxomys surifer, Maxomys whiteheadi and Leopoldamys sabanus) and one invasive (Rattus rattus) species of terrestrial murid (Muridae) in logged and unlogged forests of northern Borneo. We established four and two trapping grids in repeatedly logged and unlogged forest, respectively, for a total of 500 sampled trap sites. From these, we obtained 504 detections of the four species over 3420 trap nights. For each species, probability of detection was modelled as a function of both the structural components and disturbance level of the forest patch measured around each trap site. Each of the four species showed contrasting microhabitat preferences: M. surifer favoured increased canopy closure and intermediate ground and understorey vegetation cover; M. whiteheadi preferred increased ground vegetation cover and canopy height; L. sabanus favoured sites with larger amounts of coarse woody debris and less leaf litter; and R. rattus was associated with increased ground vegetation cover. Within logged forest, detection probabilities of the three native species did not vary significantly with level of patch disturbance, whereas that of the invasive R. rattus increased markedly in more degraded sites. This latter finding will have increasingly important implications when considering the rapid degradation of forests in the region, and the resulting expansion of suitable habitat for this competitive species.