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Habitat modification and invasive species are among the most important contemporary drivers of biodiversity loss. These two threatening processes are often studied independently and few studies have focused on how they interact to influence species declines. Here we assess the predation pressure placed on the threatened great desert skink (Liopholis kintorei) and how this interacts with fire‐induced habitat modifications. We collected daily track data of potential predators for 1 month at 30 great desert skink burrow‐systems where vegetation cover varied significantly after experimental burns. We used these data to evaluate potential predation pressure at the burrow‐system and assess whether fire influenced predator pressure. We supplemented this analysis by documenting predation via the inspection of large mammalian predator scats collected from great desert skink habitat. The level of feral cat activity at a burrow‐system entrance was significantly higher than that of any other potential predator, however fire had no effect on the visitation rates of feral cats, dingoes or large snakes to great desert skink burrow‐systems. The remains of great desert skink were found significantly more frequently in feral cat scats, compared to fox and dingo scats. We provide the first direct evidence that feral cats are a significant predator for great desert skink, thus supporting the hypothesis that feral cat predation is a key threatening process. Feral cat activity was not influenced by small‐scale experimental burns, however, this does not preclude an effect of larger scale fires and we recommend further research exploring this possible interaction.

Fire regimes are predicted to change under climate change, with associated impacts on species and ecosystems. However, the magnitude and direction of regime changes are uncertain, as will be species’ responses. For many species, how they respond will determine their medium-long-term viability. We propagate fire regime and species’ response uncertainties through a 50-year viability analysis of the great desert skink, Liopholis kintorei, in central Australia, characterizing fire regime change under three scenarios. Species’ response uncertainty was characterized with three competing models based on fire and habitat variables, fitted to 11 years of occupancy data. We evaluate fire management options for conserving the species, based on their robustness to uncertainty about fire and species’ response. Efforts to minimize the frequency and size of fires provides the most consistent improvements to species’ persistence. We show that disentangling important from unimportant uncertainties enables conservation managers to make more efficient, defensible decisions.