Cytochrome b is an integral membrane protein of approximately 400 amino acids and it is widely used as a region of mitochondrial DNA for determining Phylogenetic relationship between organisms due to sequence variability. It is considered to be most useful in determining relationship between families and genera. Comparative studies involving cytochrome b have resulted in new classification scheme and have been used to assign newly described species to genus as well as to deepen understanding of evolutionary relationship. The sequence variability of cytochrome b makes it most useful for the comparison of species in the same genus of the same family. The result obtained in many of phylogenetic studies in which this gene has been led to the proposition ofnew classification schemes that better reflectedthe phylogenetic relationship among the species. Furthermore cytochrome b gene will help in genus assignment of newly described species. Computational analysis of cytochrome b gene will be carried out in the current study. The sequences derived will use to identify the biological origin of samples by aligning to cytochrome b sequences entries in nucleotide databases. The analysis will give the phylogenetic relationship among the various common species of vertebrate animals.Using bioinformatics tools, structure prediction, conservation analysis and docking studies will be executed. Phylogenetic trees reconstruction determined how species are related to their ancestors of various orthologous species. Multiple sequence alignment takes place by Tree based consistency objective functions for alignment evaluation.