Ficus benghalensis and Ficus religiosa commonly known as Banyan and Peepal trees (or Bodhi) respectively, are important tropical trees that are being grown and traditionally revered throughout Indian subcontinent for thousands of years; however, DNA sequence-based genetic diversity of these trees are not yet known. In this report, phylogeography of these species using nuclear genome encoded ITS1-5.8S-ITS2 cistron, chloroplast genome encode RPS16- intron and trnL intron, and mitochondrial genome encoded COX1 gene is presented, making this one of the most comprehensive phylogenetic assessment of these trees conducted till date. Phylogeographic analysis of F. religiosa revealed a cryptic species, which later analysis confirmed as a novel species, described in this dissertation as Ficus indoensis Sp. Nov. that indicated affiliation to section Conosycea. Genetic heterogeneity of Ficus benghalensis remained very low and no apparent phylogeographic structures were detected. This study also revealed that colonies of Big Banyan tree at Adyar, Chennai, indeed are clonal, with 100% homology at all four loci investigated. Further, this investigation-having incorporated extensive taxa sampling (n=342) and four unlinked loci- resolved a number of phylogenetic structures within genus Ficus, so far the largest phylogenetic investigation conducted in this genus yet.