Multiple sequence alignment (MSA) is an important step for alignment, prediction and classification of protein sequences and their structural and behavior study. In this chapter, we have presented a novel approach for alignment of multiple protein sequences. Two different approaches such as the genetic algorithm and the biogeography based optimization technique were modified and merged to produce a hybrid algorithm (GA-BBO) for resolving multiple alignment problems of protein sequences. The results obtained by the proposed hybrid method are compared with some of the new alignment algorithm e.g., MO-strE, GAPAM, BBOMP,QBBOMSA and MOMSA-W etc. concluding that the new presented approach brings a remarkable accuracy when compared with existing methods over standard BALiBASE datasets. © 2019, Springer International Publishing AG, part of Springer Nature.