The pudu deer Pudu puda is a near-threatened mammal endemic to southern Chile and Argentina. Since this species inhabits mostly human-modified landscapes, addressing the factors that influence habitat use in such environments could aid in their conservation. We evaluated the presence of pudu deer during the spring-summer of 2020–2021 and 2021–2022 at two coastal range sites in the province of Osorno (Huellelhue Community, HC, and Los Riscos, RI) using camera traps. We applied logistic regression (LR) analysis to identify the predictor variables related to vegetation type, human perturbation, and native forest fragmentation that are correlated with the presence or absence of pudu deer as a binary response variable. In HC site, LR analysis identified the most likely top models including the fragmentation variable of the contiguity of patches (AICc = 22.73, Δi = 0.00 and wi = 0.77) with a negative effect (β = -8.573, P < 0.05). In RI locality the top model included the human perturbation variable of the distance to village (AICc = 23.37, Δi = 0.00 and wi = 0.71) with a positive effect (β = 1.805, P < 0.05). Both models accounted for a medium amount of the total variance in the response variable (Nagelkerke R2 = 51–52%). Results suggest that habitat use by pudu deer is affected by human perturbation and native forest fragmentation. Our findings indicate that maintaining a more continuous native forest or areas of native forest located far from human settlements could represent an important strategy for improving the long-term survival of the species.