The Brazilian semiarid region presents a rainy season, characterized by irregular precipitation, and a dry season. In turn, the palm tree Syagrus coronata is a key species from this region, being highly exploited by local human populations. Understanding how climate and landscape changes have affected the distribution of genetic diversity among and within palm tree populations is essential to propose effective conservation strategies. Therefore, we investigated the historical climate suitability and estimated the genetic diversity and population structure along the natural range of S. coronata based on microsatellite markers. In spite of high exploitation, high levels of genetic diversity were usually observed in adult specimens of S. coronata. The most genetically diverse populations are located in the center of the geographic distribution, namely: Brumado (BRU), Campos de Sao Joao (CSJ) and Itaberaba (ITA), overlapped with ancient glacial refugia. In addition, signs of population expansion from the Late Interglacial Period to present days were identified, including evidence of new occurrence outside their original habitat. The high diversity and moderate structure of S. coronata contrasts with recent landscape fragmentation, suggesting that long-term monitoring and proper management of genetic variation should be performed in this palm tree. Furthermore, the expansion in the natural range of an endemic palm tree from semiarid to other biomes represents an alert on current climate changes and desertification processes in tropical regions.