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Habitat models constitute useful instruments for understanding species-habitat interactions and can constitute helpful conservation tools. The Upper Paraná Atlantic Forest (UPAF) of South America still holds the world’s southernmost jaguar (Panthera onca) population. Our aims were: (i) to test several a priori hypotheses on the factors affecting jaguar persistence in this region, (ii) to map habitat suitability and identify areas with potentially conflicting habitat conditions, and (iii) to identify priority areas for management and improve the conservation initiatives for jaguars and the UPAF. Following an information-theoretic approach, we used presence records of jaguars and pseudo-absences in generalized linear models. We structured hypotheses into two groups which demand different management actions: land cover and human persecution. The best model of each group was used to develop a two-dimensional habitat model. Jaguar persistence was favoured by current and historical native forest cover, and hindered by human land uses. Protection favoured jaguar presence whereas human accessibility and high human population density had negative effects. The two-dimensional model suggests that