An efficient recursive approach is proposed in this paper that would not only find the multiple sequences alignment for protein sequence but also provides means for consideration of gaps between them. MSAs are usually scored with the Sum-of-Pairs (SP) function and the Match Column (MC) function, but exact SP and MC for MSA is known to be NP-Hard. Therefore in this paper, a heuristic method is used to solve MSA problem using genetic algorithm. Three different operators were proposed, one type of selection operator, one types of crossover operators and one type of mutation operator for feasible alignment of protein sequences. The input variables (e.g. Strands) of the program are user dependant and internal calculations are performed in recursive fashion to add intelligence to the input Strands. Experimental results of benchmarks from the BAliBASE 3.0 shows that the strategy adopted in the study is able to obtain better results, when compared to the traditional MSA tools. © 2015, Global Research Online. All rights reserved.