Magnaporthe oryzae is a plant pathogenic fungus and model organism due to its agricultural impact and tractability that causes severe blast disease affecting rice. Due to its complex cryptic species, VNTRs and complex polyphyletic lineage due to the presence of many transposable elements. In the present study the internal transcribed spacers (ITS) of the ribosomal DNA sequences were used to characterize the 40 monoconidial M. oryzae strains from blast disease samples of the Telangana. Using DNAsp, performed a population genetics study on the sequencing data and discovered that rDNA sequence variation was highly polymorphic, with 0.01521 nucleotide diversity. In the present investigation 8 haplotype groups with Haplotype 2 (Hap_2) were reported to have with a broader genetic base. With a D value of −2.660 and a P 0.05 Tajima's neutrality test, the haplotype diversity is 0.52317, implying that there are variations in the pathogen isolates' sequences. The pathogen's apparent clonal reproductive behaviour was in contrast to the observed population structure, which suggested that genetic recombination may still be occurring within the pathogen population. The total number of variable sites (S) and mutations (Eta) were 63 and 73 respectively. Further, a haplotype network was constructed for the comparison of genealogical relationship's among (ITS) allele's using Population analysis with reticulate trees (PopArt software) a population genetics software to visualize the broader genetic base and genetic drift among the samples collected from the various locations of Telangana.