An attempt was conducted to understand the genetic population structure and historic demography of Indian mackerel, Rastrelliger kanagurta from Indian peninsular waters using mitochondrial DNA markers. A total of 241 sequences of mitochondrial control region and 271 sequences of mitochondrial ATPase gene region were amplified and analyzed in Indian mackerels collected from 10 different locations along Indian coast resulting in 123 and 155 haplotypes respectively. In addition, control region sequences representing samples from Thailand downloaded from NCBI were also used for analysis. Significant genetic differentiation (�ST value of 0.38; P < 0.001) was recorded between samples from mainland India, Portblair and Thailand when both control region and ATPase gene sequences were analyzed. Whilst, �ST values were not significant when analyses were carried out between samples collected from mainland India. Oceanographic and environmental barriers between mainland India, Portblair and Thailand contribute to limited larval dispersal and restricted mixing between populations resulting in subtle genetic differentiation. The lack of genetic subdivision between populations from mainland India indicates adequate gene flow and mixing within Indian waters. Bayesian skyline plots revealed a history of population expansion taken place approximately 10000 years ago coinciding with the time after the last glacial maximum or early Holocene. Intensification of monsoon events after the last glacial maximum or early Holocene along the Indian subcontinent contributed to increased productivity in the Tropical Indian Ocean and consequent demographic expansion of mackerel populations historically. Management measures for Indian mackerel populations could be devised regionally so as to conserve intra-specific diversity and biocomplexity of this important resource.