Deforestation decreases both biodiversity and other ecosystem services that forests provide, such as climate regulation and water regulation. Given high rates of deforestation across the world, especially in tropical forests, international efforts have implemented forest protection programs to offer payments for ecosystem services (PES). Monitoring the performance of these programs over large areas can be difficult, especially in areas with limited satellite data availability. Furthermore, even when deforestation data is available, it is often unclear how deforestation has affected levels of forest fragmentation or habitat availability for wildlife species including predators. The goal of this dissertation was to monitor forest fragmentation and deforestation in tropical forests, and to map potential habitat and its connectivity for jaguars. I found a gradient of forest fragmentation across Mexico, moving from lower levels of fragmentation in the north, to higher levels of fragmentation in the south and east of the country. The highest levels of forest core were lost within tropical forests. Forests that were enrolled in the PES program had less fragmentation than those that were not. To improve detection of deforestation, I combined Landsat and MODIS images to assess deforestation in areas with strong phenology, and where original Landsat imagery was lacking. From this assessment, I calculated deforestation rates across Mexico, which confirmed the gradient of low deforestation in the north to high deforestation in the south. At the local level, I generated a potential habitat suitability map for jaguars in the Sierra Gorda Biosphere Reserve in Central Mexico and identified the areas that were most important for habitat connectivity. Moreover, I developed new methods to identify optimal thresholds of minimum patch size and habitat suitability for connectivity analyses. My approaches can be easily transferred to other systems where there is a need to assess deforestation with limited imagery, forest fragmentation, and habitat connectivity.