In the past few years, the Multiple Sequence Alignment (MSA) related problems has gained wide attractions of scientists and biologists as it is one of the major tools to find the structural and behavioral nature of Biomolecules. Furthermore, MSA can also be utilized for gene regulation networks, protein structure prediction, homology searches, genomic annotation or functional genomics. In this paper, we purpose a new nature and bio-inspired algorithm, known as the Whale Optimization Algorithm for MSA (WOAMSA). The algorithm works on the principle of bubble-net hunting nature of the whale with the help of objective function we tried to solve the MSA problems of protein sequences. In order to focus on the effectiveness of the presented approach, we used BALiBASE benchmarks dataset. At the last, we have compared the obtained result for WOAMSA with other standard methods mentioned in the literature. After comparison, it was concluded that the presented approach is better (in terms of obtained scores) when compared with other methods available in the considered datasets. © 2020, Springer Nature Switzerland AG.