During the last ten years, the problem of subterranean termites in Alexandria, Egypt has worsened, causing great economic losses. Throughout our study to survey the termite species in Alexandria, a species was found that differed from any of the previously recorded ones in Egypt. The aim of this study was to identify this invasive subterranean species in the region. Samples were collected from infested buildings and trees, and their morphological characteristics along with their DNA barcoding loci (COII, 18S and 28S) were determined. Moreover, phylogenetic comparison with other related species were also considered for the most accurate identification. The analysis of all the previously mentioned parameters proved that it is Coptotermes sp. This genus is identified and recorded for the first time in Egypt and North Africa. This study demonstrates that the combination of molecular and morphological methods is essential for accurate species identification, which aids in the correct control of destructive pests.