In the frame of phylogeographic studies of small terrestrial mammals in eastern Africa, we observed conspicuous spatial genetic patterns in multiple savannahs' taxa (either within species or among closely related species). Most frequently, the divides among main lineages were concordant with Eastern Arc Mountains (EAM) and with rift valleys filled by lakes Malawi and Rukwa. Importance of these biogeographical divides was analysed by a new approach based on graph theory, using genetic data from 12 genera and 37 species or intraspecific lineages of rodents and shrews. As expected, the algorithm clearly defined three assemblages of taxa separated by a Y-shaped divide Malawi-Rukwa-EAM. Geographic distribution of sister taxa suggests major division between communities of northern (i.e. north-central Tanzania) and southern savannahs. In the latter, the assemblage east of EAM and Malawi Lake is only an offshoot of more widespread western (Zambian) one. The results of comparative phylo(bio-)geographical analysis therefore clearly indicate the importance of EAM and East-African rift valleys in forming the communities of small mammals living in non-forested habitats. Due to different evolutionary ages of particular taxa (approx. from 300 kya to 3 Mya), and absence of obvious current barriers to gene flow among defined regions, we speculate that the observed structure is driven by repeated extinctions of savannah community at detected divides. Alternatively, the role of long-term differences in climate and vegetation of three savannah regions separated by the Y-shape divide cannot be ruled out.