Understanding how historical and current environmental suitability and human impacts affect the genetic diversity on a large scale is essential to species management planning. However, most studies in conservation genetics are carried out at a local or regional scale and rarely on broad spatial scales such as an entire biome. We evaluated the relative contribution of historical and current environmental suitability, current landscape features and human impacts to explain genetic diversity, allelic richness and inbreeding variation among populations, using Euterpe edulis and the Atlantic forest as the model system. We fitted linear mixed models within a multiple competing hypotheses approach with model selection based on Akaike's Information Criteria. We showed that overall genetic diversity was lower in sites with absence of large seed dispersers and higher in sites with historically stable climate. Both seedling and adults showed to be negatively influenced by human impact factors; with adults mainly affected by the reduction of forest cover while seedlings by the loss of large seed dispersers. Thus, the current pattern of genetic diversity in E. edulis is the result of historical instability during the mid-Holocene and recent anthropogenic impacts, mainly those that affect important ecological process such as seed dispersal. Thus, an efficient plan for species conservation must account for human impacts and environmental suitability and also assess the genetic diversity of seedlings and adults in fragmented landscapes.