Understanding how species respond to changes in their environment is crucial for effective conservation efforts, particularly in vulnerable ecoregions like the Uruguayan Savannah in Brazil and Uruguay. Here, we focused on two often overlooked species, the South American coati (Nasua nasua) and Molina's hog-nosed skunk (Conepaptus chinga), deploying 79 cameras across 15 areas in both the Brazilian and Uruguayan sectors of the ecoregion. Using occupancy models, we investigated the influence of different land cover types (forests, grasslands, farmland, and silviculture) and human density on the presence of these species. We tested the activity pattern uniformity for each species. We looked at the landscape transition history. Furthermore, we also generated innovative occupancy maps to better understand and guide policies and actions for these species. The coati occupancy exhibited a positive relation with forest areas but a negative correlation with grasslands and crop farming areas (p<0.05). The skunk presented a positive response to grassland and crop farming areas but a negative response to forest areas (p<0.05). The South American coati occupancy was estimated at approximately 0.141 (0.041 – 0.420), while for Molina’s hog-nosed skunks, it was 0.377 (0.200 – 0.610). Despite the coati's use of open areas, it demonstrated a stronger association with natural forests than altered landscapes. In contrast, Molina's hog-nosed skunk displayed adaptability, persisting in altered environments. In conclusion, our findings underscore the urgency of prioritizing conservation efforts for coatis, while highlighting the skunk's resilience to landscape alterations. This knowledge can guide targeted conservation plans for these species in threatened ecoregions.