Hypertrophic cardiomyopathy is a condition in which the myocardial muscles become thickened without an apparent cause. It exhibits the prevalence of 1/500 globally. Eighteen samples from four families of maternally inherited HCM were collected, based on their clinical records. Three mitochondrial encoded genes 16S-rRNA (MT-RNR2), tRNAIle (MT-TI) and tRNALeu (MT-TL1) were targeted for analysis of mutation. Genomic DNA was extracted from buccal swab using Phenol: Chloroform: protocol. The target genes were amplified via polymerase chain reaction (PCR). The amplified gene products were sequenced and compared with the revised Cambridge Reference Sequence (rCRS) Accession-No. N_012920.1. Four mutations in 16S-rRNA gene have been identified viz mt-2552T>A, mt-1811A>G, mt-1888A>G and mt-2467A>T and two are novel, mt- 2552T>A and mt-2467A>T while others have been previously reported, in patients of German and French population. For the first time, the mt-1888A>G and mt-1811A>G mutation in MT-RNR2 gene have been observed in patients of HCM in the Pakistani population and even not found in the control group of the same families. No mutation in mt-DNA encoded tRNAIle, and tRNALeu genes were observed, the mutations detected in mt-DNA encoded 16S-rRNA gene are the pathogenic mutations associated with HCM in Pakistani population.