In this study mitochondrial 16S ribosomal DNA sequences were isolated by PCR, sequenced and used to infer a molecular phylogeny.Termites were sampled from different localities of Pakistan and analysed morphologically.DNA was extracted from individual whole alcohol preserved worker termites. That were freeze dried, using DNeasy tissue kit. The DNA extraction protocols were defined.Then DNA Sequencing was done, DNA sequence alignments also done using Clustral method with weighted residue weight table in DNA star software.This study would provide baseline data on genotypic variability for different termite populations from different localities.Microsatellite genotyping utilizating high resolution non denaturing poly acrylamide gel electrophorsis was a qualitative method of evaluating allelic and genotyping diversity to determine colony distinction in termites also. So following the criteria described above, we would provide a DNA based identification system of termites in Pakistan.