One of the remarkable achievements of modern biology has been the development of accurate and reliable technologies for the rapid screening of DNA sequence variations. Molecular identification and DNA barcoding is a taxonomic method that can be used to identify a species, including an unknown one. Mitochondrial genome is most extensively studied genomic system in insects. In this review, we describe the various molecular works that have been done on Indian Muscidae. It can be concluded that, the molecular studies are not common for the Indian muscid species and only few studies have been conducted. A lot of work still has to be done in India with more species and molecular markers.