Multiple Sequence Alignment (MSA) problem based on aligning three or more biological sequences by considering the maximization of similarity is one of the most important problem in bioinformatics. In this paper, a new Artificial Bee Colony (ABC) algorithm inspired by the intelligent foraging behavior of honey bees is proposed to generate optimum solutions. Multiple alignments obtained by the proposed ABC algorithm are compared with the basic ABC algorithm, Genetic algorithm and Particle Swarm Optimization algorithm in the literature over the Relative Sum of Pairs (SPS) score. From the simulation results, it is concluded that the modifications made on the employed and onlooker bee phases have increased the quality of the alignments.