Identifying and prioritising naturally occurring within-species diversity, which may correlate with local adaptations or vicariance, is an integral part of conservation planning. Using non-invasive sampling and a panel of 11 microsatellites on 158 individual tigers from a pan India sample, our evaluation revealed three population clusters in India: unique North-Eastern tigers, a combined cluster of Western Ghats, Western India and Terai tigers, and a mixed cluster from Central India. At further population division, tigers from Odisha,
Valmiki and southern Western Ghats were distinct. Central Indian tigers were most diverse, but showed the highest level of local structuring, suggestive of human induced fragmentation. We show that tigers in India are genetically structured and some clusters are unique. Considering a combined analysis of population size, genetic diversity and uniqueness, tigers from the North-East hills, and southern Western Ghats emerge as conservation priorities. We propose reintroductions and supplementation of tigers be done among the same broad genetic clusters. Restoration and management of habitat corridors is vital for anthropogenically fragmented Central Indian populations. This study suggests a paradigm shift from indiscriminately doubling tiger numbers to prioritising conservation of naturally occurring diversity amongst tigers, to retain their full evolutionary potential, while managing to mitigate anthropogenic induced genetic structuring.