Bacteriocins are therapeutic, biocontrolling and proteinaceous molecules produced by various lineages of bacteria. It is synthesized under the control of genetic mechanisms and develops their lethal action on the microbial cell by multiples mechanisms. In this study we evaluated the evolutionary relationship between bacteriocin producing gram positive and gram negative bacteria and modeling of their protein molecules. To find out these phylogenetic trees were constructed on the basis of homology between the protein sequences. Phylogenetic tree for gram negative sequences shown medium bootstrapped values even less than 50 and these strain were not much related with one another as in the case of gram positive sequences. In gram positive most were found with bootstrapped value equal to 100. Thus it was observed that they having intra high region and inter low region of homology between them . It was concluded from modeling of proteins that were shown rich with alpha and beta sheets that leads stability of protein.Thus coding sequences for alpha and B sheets remain more conserved in gram positive as compare to gram negative during period of evolutions.