Pakistan has approximately 53.79 million goats and 26.49 million of Sheep. Goats AND Sheep are kept for milk meat and wool production and contribute significantly to the income of the farmers. Thirty recognized breeds of goats and twenty eight breeds of sheep found in Pakistan. Improvement of livestock productivity per unit animal remains the primary concern of research and development efforts. The purpose of this research work was the genetic improvement of Sheep and Goat breeds. In this present study of Goat and Sheep, Ten different breeds of Goat: Barbari, Beetal, Pahari hairy, Kamori, Damani, Khurasani, L.Hairy, Teddy, Lehri goat, Nachi and ten different breeds of Sheep: Bulkhi, Dumari, Kachi, Kaghani, Salt range, Awassi, Thalli, Lohi, Krakul, Shenwari were selected but the genetic data of different goat and sheep breeds is lacking which need to be established for their genetic characterization. Blood samples of unrelated true representatives of all breeds were collected from their respective home tract. DNA was extracted with the use of standard protocol and amplification of the mitochondrial. D-loop and Cytochrome b region was done with specific primers in Molecular Cytogenetics and Genomics Laboratory in the deptt of Molecular Biology and Biotechnology. Sequencing of amplified portion of mt.DNA D-loop and Cytochrome b was done. Sequences were analyzed with the help of software blast 2 sequence. Single Nucleotide Polymorphisms (SNPs) were identified and comparison of 50, 50 samples of Goats and Sheep of Cytochrome b gene and mitochondrial D-loop region were compared with their respective reference sequences. Genetic identity between ten goat breeds were calculated by BioEdit. 50 goat haplotypes and 49 sheep hapoltypes were identified. All haplotypes were rich in AT contents. 22 conserved region were identified which were common in Goats and Sheep (BioEdit, 7.0). Goals and Sheep sequence comparison was made by using sheep Ovis aries as a referenece. 405 varibale sites were already present in Goat and Sheep. Capra hircus (AF533441) had 41 insertions and 9 deletions with respect to Ovis aries (AFO 10406.1). Phylogenetic tree was constrncted using Mega 4.1 software showing the relationships between different haplotypes. Haplotpes of this research work were compared with some world wide haplotypes of Goat and Sheep separately. Goat showed very close relationship with haplotypes of Africa, Asia and Europe, while Sheep showed close relation with Europeaon and Asian haplotypes. Both Goat and Sheep seemed to have domestication from Asia. From analysis of Goat and Sheep with their wild reported haplotypes, it was confirmed that Goats and Sheep used in this research work were domestic and had close relation with Capra aegagrus and Capra sibrica was present at the bottom of phylogenetic tree. While Sheep (Ovis aries) showed a close relation with wild Mouflon (Ovis musimon).