Fungus growing termites is a unique group of termites that can grow mutualistic fungi from Basidiomycota: Termitomyces inside their nest. This group of termites has an important ecological role as a major decomposer. However, comprehensive study of fungus-growing termites is limited in Thailand and the complex termites-fungus relationship is a challenging issue to study. This research was aimed to identify the species of termites and fungal symbionts using DNA barcoding, to compare the molecular results with morphological identification, and to gain insights into the co-evolutionary relationship by constructing co-cladogenesis analysis from the termites and the fungal symbionts. Four termite species (Macrotermes annandalei, Odontotermes feae, Ancistrotermes pakistanicus and Ancistrotermes sp.) from four Sakaerat and two Chulabhorn colonies were identified based on the BLAST-N of cytochrome oxidase sub-unit I (COI) sequence and morphological identification. The partial COI sequence of O. feae identified in this study is the first record of this species deposited into the NCBI nucleotide database. Molecular identification of the fungi were conducted by using nuclear ribosomal internal transcribed spacer (ITS) region. The results showed that those six termite colonies grew specifically the fungal genus Termitomyces. Three genetic groups of Termitomyces i.e. Group 1, Group 2 (T. cylindricus), and Group 6, were present among the six colonies. Molecular identification was confidently supported by morphological identification of termite samples, at least up to the genus level. High host-symbionts specificity is considerably observed within some clades on paired termite-fungus phylogeny. However, more sampling is needed for the more confident result.