Deccan College (India) and Institute of Forensic Science, Seoul National University (South Korea) plan to make collaboration on bioarchaeological researches in both countries. In such an effort, researchers in both institute tried to study on the biological samples from Rakhigarhi site, one of the largest metropolitan cites of ancient Harappan civilization. Using the animal bones collected from the site, an attempt was made to extract ancient DNA by a modified phenol- chloroform method. For analysis of aDNA from the cattle bones of Rakhigarhi site, we tried to develop a multiplex amplification system of Bos taurus mtDNA genome from much recent Joseon period cattle bone samples. Our study would be done using next generation sequencing technique; and bioinformatics analysis will be performed on the data. Ours will be an invaluable stepping stone for future studies on the genetic diversity and structure of Bos taurus and Bos indicus of Asian continent.