This paper proposes a new hierarchical land classification system for the mapping of species distribution at national or regional scales. Our integrative framework incorporates two hierarchical levels inferred from historical, climatic, geomorphological and geological attributes. The feasibility of this proposal is based on the use of historical collections and literature data, as well as on its ability to combine old low-precision data with more recent records of higher resolution. The system is set up for vascular plants, but it can also be used for other taxonomic groups. Furthermore, it has the potential for application to the whole Mediterranean region because it is based on information that is generally available in all Mediterranean countries. This model is tested with the distribution of loci classici of the Italian endemic plants occurring in Sicily.