Definitions of Biodiversity that encompass multiple levels of the biological hierarchy are common and fulfill theoretical and conservation expectations. However, these definitions are usually not fully operational because these levels are usually analyzed independently. We understand that the difficulties in integrating concepts and methods for distinct "Fundamental Biodiversity Units" (FBUs) for analyses, including genes, haplotypes or neutral molecular variants, species, biomes or ecosystem, arise both because of operational and conceptual difficulties in dealing with the evolutionary continuum and because of 'sociological' issues regarding how different research traditions in Ecology and Evolutionary Biology deal with these different FBUs. Here we explore some common patterns of geographic variation in FBUs at different hierarchical levels, starting from the conceptual view by which evolution give rises to a continuum of biodiversity. We seek for an integrated methodological and conceptual framework to study FBUs, searching for the relationships and commonalities of concepts and methods traditionally developed to evaluate patterns and processes at a given level of the biological hierarchy. We point out several cases where conceptual and theoretical advances have been made by using an integrated perspective based for FBUs, for the analysis of broad-scale gradients in richness, distance decay similarity and systematic conservation planning. We conclude by stating that the recognition of an integrated approach that takes the evolutionary continuum into account may be an important step to mitigate biodiversity loss.