A key question that remains unexplored in evolutionary biogeography is how much of the phylogeny for multiple taxonomic groups is present in a region?  Here, we propose a multi-level framework to enhance our ability to identify areas of lineages congruence across multiple groups. The aims were to create a tool that identify unique phylogenetic regions across multiple taxonomic groups and also that helps to improve conservation prioritization of lineages and not taxonomic species only. In order to test our framework, we used species occurrence and phylogenies corresponding to five test groups: fish, frogs, Acacias, eucalypts and plant genera. The total number of analysed occurrence records is over 70,000 with more than 500 species which comprises about 700 genera. We applied the method in the largest Australian river system, Murray-Darling Basin region, because it has a high relevance for human colonisation and therefore conservation.  We argue that such approaches are highly useful to improve conservation prioritization at broad geographical level which is essential to enhance our understanding of diversity distribution under climate change.  The initial results successfully identified areas of concurrent centres of endemism as well as phylogenetic diversity that were classified as unique phylogenetic regions. Such areas were not previously identified as important by traditional diversity assessment methods. Hence, that information enabled us to propose for the first time a genetic-based regionalization for the MDB and therefore concept prove our framework.