Macrotermes gilvus is a termite species of immense ecological value due to its crucial role in nutrient turnover and soil formation. A critical need for ecological research and pest management strategies is to gain an understanding of its genetic diversity as well as evolutionary relationships. This project used molecular phylogenetic analysis of M. gilvus genetic make-up through DNA barcoding the cytochrome oxidase I (COI) gene. Simple Sequence Repeats analysis indicates that Macrotermes carbonarius holds much less variation in terms of polymorphism along with other parameters such frequency changes than M. gilvus in local populations. Using COBF and COBR primers we were amplified a 400 base pair (bp) fragment of the COI gene by polymerase chain reaction (PCR), successfully gaining a discrete amplicon band on an agarose gel. The PCR product was then purified to remove contaminants. Forward and reverse DNA sequencing reactions were performed with the same primers of the BDT v3.1 Cycle Sequencing Kit on an ABI 3730xl Genetic Analyzer following procedures detailed elsewhere.