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Microgyne trifurcata is a rare native plant species from one of the areas with the highest human impact on the environment in southern South America. Its habitat, mostly grasslands suitable for agriculture, has been increasingly covered by crops since the late 1800s. Microgyne trifurcata provides an excellent case study to understand how different environmental variables have affected the distribution area of a rare species. This study aims to estimate the impact of topoclimatic and land-use changes in the distribution of Microgyne trifurcata throughout the twentieth century. We carried out recent past and present distribution modeling using the Ensembles of Small Models (ESM) methodology. In this spatio-temporal study, we included climatic, topographic, and land-use variables. We classified the occurrences into two periods of the twentieth century. The first dates from 1901 to 1940, and the second, from 1960 to 2000, when the main cropping changes of the area occurred. The projected area between 1960 and 2000 provides for this species new suitable habitats toward the northeast of the area of study. Our results highlight the importance of assessing the combined impacts of climate and land-use changes on species distributions over time. This study shows that the potential area of Microgyne trifurcata decreased and underwent fragmentation throughout the twentieth century when these variables combined are used to model its distribution. Our outcomes prompt future studies on the vulnerability of Microgyne trifurcata to outline conservation strategies. [ABSTRACT FROM AUTHOR]