Aim: The objective of this study is to infer into the protein sequences in order to solve the multiple sequence alignment problem of protein sequences using genetic algorithm optimizing technique. Methods: In this work, a genetic algorithm based approach has been presented and used accordingly. Different genetic operators along with a fitness function is proposed so as to obtain a optimal quality solutions for protein sequences. Results & Discussions: Results based on various parameters have been recorded and analyzed over a set of clusters orthologous groups of proteins and were compared with the results obtained with other alignment algorithms, e.g. Clustal W and Central Star algorithms. The obtained results show the superiority of the proposed technique as it achieves betters solution in terms of scores, when compared with the methods mention above. © 2015, Pharmainfo Publications. All rights reserved.