The presence of the yellow-necked drywood termite, Kalotermes flavicollis Fabr., has been reported along most of the Mediterranean coasts of Europe, Africa and Asia. While morphological and genetic data exist on European K. flavicollis populations from western and central Mediterranean regions, data on eastern Mediterranean Kalotermes are scarce, and no genetic data exist to date. In this study, we analyzed 17 Kalotermes sp. colonies from 11 localities in the Levant (Cyprus, Lebanon, and Israel), in order to characterize genetically (mitochondrial DNA: COII, 16S, and control region) these populations. We found that samples from the Levant are genetically different from K. flavicollis, with distance values falling in the range of interspecific distances. In the phylogeny of European Kalotermes populations, samples from the Levant form a clade of their own, sister to a clade including K. flavicollis and Kalotermes italicus. Inside the eastern Mediterranean clade, all the samples from Cyprus are included in a well-supported subclade, suggesting that the colonization of the island might have occurred in a single event. These findings show that the populations we examined do not belong to the species K. flavicollis, but to a new species peculiar to the Levant, that we describe as Kalotermes phoeniciae sp. nov. It is possible that previous reports of K. flavicollis in this region can be attributed to K. phoeniciae.