Fragmentation transforms natural habitats into a set of structurally and functionally differentiated small and separated patches, and causes the loss of connectivity among populations. In this study, we used a multi-temporal approach (1986, 2011 and 2016), to analyze the patterns of habitat fragmentation and to identify critical zones for the maintenance of habitat connectivity of two focal pine species (Pinus pseudostrobus and P. montezumae) with the broadest distribution and highest economic importance in the temperate forests of the Meseta Purépecha, in Michoacán, Mexico. This eco-region is currently one of the most threatened in terms of habitat degradation and extinction of forest communities. From a supervised classification of satellite images, land use coverage classes were selected and used as a basis to analyze the degree of landscape fragmentation using configuration and composition metrics and landscape connectivity based on the graph-theory approach. The fragmentation metrics suggested an increase in agricultural coverage (10.81%; fruits crop, mainly avocado), while the coverage of the forest showed a reduction (15.06%) and fragmentation throughout the study period. The landscape connectivity is lower (16.3% on average) and showed two highly important zones (Uruapan and Tancítaro) and one zone of high importance (Pátzcuaro) to maintain connectivity, considering three different dispersion distances (0.5, 5.0 and 10 km) for the species analyzed. We propose these three zones as potential habitat stepping stones to promote overall landscape connectivity, offering primary habitats and possible ecological resilience for this important forest ecosystem.