Arid and semi-arid mammals experience irregular rainfall and resource pulses from year to year. Consequently, some species fluctuate in persistence and abundance between years, while other (often coexisting) species remain relatively constant. In the semi-arid mallee environment of Eyre Peninsula South Australia, two dasyurid marsupials, the mallee ningaui (Ningaui yvonneae) and the sandhill dunnart (Sminthopsis psammophila), are sympatric and exhibit a similar life history strategy. However, N. yvonneae is relatively common and stable in abundance, while S. psammophila is considered rare and its abundance fluctuates both temporally and spatially. We were interested in ascertaining whether habitat preferences and use by these species differed, and whether this might help explain variability in their temporal and spatial abundances. We used data obtained at two spatial scales; broad-scale trapping at 11 sites (using pitfall and aluminium box traps) and fine-scale (direct) observations of foraging. Observational data were collected by recording behaviour and movements while animals foraged at night time, with the aid of fluorescent chemi-tags affixed to individuals. Habitat data were collected at each scale, and generalised linear modelling was used to understand habitat preferences. The combination of data from broad and fine scale habitat use may provide insights into the drivers behind population abundance in these dasyurid marsupials, and afford valuable information to consider when managing areas for the persistence of mammal assemblages.