The essential variables of biodiversity are a set of attributes that have been internationally proposed to unify and make more efficient the monitoring of biodiversity. Remote sensing are valuable tool for monitoring these variables. This work aims to describe a methodological framework to monitor the essential biodiversity variable “species distributions”, through the integration of national products of land cover and species distribution models, the last is available on the web application BioModelos. The proposed methodology was applied for two species of the genus Zamia to illustrate the potential use of the outcomes. By intersecting the distribution models of these species with forest cover geographic layers for the period 1990-2015, it was possible to analyze the extent of change in potential habitat for both species. It was found that such change is mainly related to technical features of remote sensing products and with anthropic activities associated with deforestation. Additionally, we assessed the expected extent of suitable habitat for both species in 2030 based on forest cover change scenarios, evidencing the need to support the adoption of planning exercises in which the loss of biodiversity due to deterioration and loss of habitat will be minimized. Finally, we identified the presence of two deforestation areas in the distributions of these two species that may represent an important threat to their persistence in the future. The methodology proposed here, which integrates expert knowledge, the development of species distribution models, and remote sensing products to monitor land cover change, is an important input to assess species extinction risk and to develop a system of early warnings therefore biodiversity loss may be estimated at national level.