The biodiversity of the European termite Kalotermes flavicollis is here studied through the analysis of mitochondrial (303 bp of control region and 912 bp of COI/tRNA(Leu)/COII) and nuclear (five microsatellite and 20 Inter-SINE loci) markers on 18 colonies collected in Southern France, Corsica, Sardinia, peninsular Italy, the Balkans and Greece. Different statistical analyses (Bayesian phylogenetic analysis,parsimony network, F-statistics, PCA) were performed. Mitochondrial sequences produced an unresolved polytomy including samples from peninsular Italy, Balkans and Greece, and three main clades: southern France, Corsica-Sardinia and Portoscuso(SW Sardinia). Nuclear markers confirm these data, further highlighting a more significant divergence at the regional scale. The results obtained for the peri-Tyrrhenian area agree with major paleogeographic and paleoclimatic events that shaped the biodiversity of the local fauna. K. flavicollis biodiversity and its phylogeographic pattern are also evaluated in the light of the data available for the other native European termite taxon (genus Reticulitermes), in order to produce a more complete scenario of the Mediterranean. In the area comprised between southern France and Italy, the degree of diversity is similar; however, in the eastern area, while K. flavicollis is differentiated only at the population level, the genus Reticulitermes comprises at least six entities of specific and/or subspecific level. This discrepancy may be explained by taking into account the different evolutionary histories of the two taxa.