Leather and leather products are the most traded commodities and play a significant role in the world’s economy. The traditional tanning methods and the high quality of Indian leathers receive global appreciation. The existing leather manufacturing methods made a significant loss in epidermal constituents which impact the commercial importance of the animal species. Embossing techniques could potentially contribute to an increase in fraudulent activities. Since the fate of genetic material in finished leather is questionable, which poses a challenge to the molecular approach for identification. In order to obviate the problem, the present study aims to recover amplifiable mtDNA from leather products and focus on developing probes and primers for RT-PCR, which significantly enhance cross-specificity. Data mining and phylogenetic analyses of mtDNA genes (12S rRNA, COI, and Cyt b) for Indian Ovis aries skins exhibit the taxonomic positions and the intraspecies relationships, thereby facilitating the probes desigining. The results indicate that the maximum intraspecies genetic divergence observed within 12S rRNA, followed by COI and Cyt b. Since the availability of genetic sequences with reference to Cyt b is comparatively large (602), primers and probes were designed for Cyt b. The RT-PCR analysis of finished Ovis aries leather mtDNA samples yield a ct value in the range of 22–23 cycles, even with a minimum quantity of template DNA as low as 0.3 ng. Results on the cross-specificity analysis are highly encouraging. Hence, it is feasible to identify genuine Ovis aries leather using mtDNA instilling confidence in the export of leather.