The increased availability of phylogenetic, morphological, and geographic information from different biological groups has allowed for the testing of several scenarios on the origin and assembly of the biota around the world. The biogeographical approaches used to understand the origin of the Yucatan Peninsula Biotic Province (YPBP) flora were previously based on floristic comparisons and do not consider the phylogenetic relationships among taxa, complicating the understanding of their biogeographical history. In order to improve the understanding of biogeographical and evolutionary processes implied in the occurrence of the endemic flora of the YPBP, we constructed a geobiotic scenario, which integrates lineage divergence events obtained from previous phylogenetic and biogeographical studies, along with geological/tectonic and climatic events occurring in the area. To strengthen the biogeographical hypotheses, we constructed a phylogenetic tree as a framework for an approximation of the periods of history with the greatest influence on the evolution of the flora. Additionally, we searched for morphological traits of relevance for dispersal, establishment, and adaptation to the current environmental conditions of the YPBP. The evidence gathered in the present work strongly suggests that the origin of the endemic flora of the YPBP has been driven by various factors and processes that occurred at different times in the history of the Earth (mainly in the Pliocene and early Pleistocene). These include hybridization, isolation after long-distance dispersal from the Antilles, as well as the influence of environmental changes during the Pleistocene. Those climatic fluctuations reduced the geographic range of some ancestral lineages, leading to geographic isolation of populations in the northern part of the YPBP, where the climate has been more stable over time.