Goat and Sheep have a very important role in the live stock sector. They are being used for milk, meat and wool production. There is need for the genetic improvement of goat and sheep breeds. Twenty breeds of goat and sheep were studied for evolutionary study and specie differentiation. Complete mitochondrial d-loop and cytochrome b region was sequenced. Single Nucleotide Polymorphism was studied and all the sequences of goat and sheep were multiple aligned to see the specie differentiation. Phylogenetic analysis of goat and sheep breeds were performed with their respective world wide reported haplotypes. Both goat and sheep seemed to have domestication from Asia. Goat and sheep evolutionary analysis with wild haplotypes showed that presently both species are domestic; goat has close relationship with Capra agagrous while sheep showed close relationship with wild Mouflon (Ovis musimon).