Rabies, a fatal zoonotic viral encephalitis kills tens of thousands of people each year in India, representing one third of the estimated global rabies burden. A detailed understanding of the molecular epidemiology of the Rabies lyssavirus (RABV) in India is limited due to the low availability of sequences from the country. In this study we examined the feasibility of direct sequencing of clinical samples (archived human and canine brain tissues, 10 each), for detection and recovery of whole genome sequences of RABV, on the MinION – single molecule nanopore sequencing device. Using an amplicon-based approach, complete RABV genomes were recovered from all the 20 samples, archived from 2003 to 2019, from 4 southern states of India. Phylogenetic analysis revealed that all 20 sequences from this study belonged to the Arctic-like (AL) 1a lineage. Divergence estimation of sequences revealed that all the circulating RABV strains within India are diverged in last 60 years from the previous ancestor. The genetic relatedness and close clustering of the sequences in the study suggests the continued propagation of AL1a in the region, across state boundaries. Genomic surveillance can provide unique insights into rabies spread and persistence that can direct control efforts in India.