Multiple sequence alignment(MSA), known as NP-complete combinatorial optimization problem, is one of the most important and challenging tasks in bioinformatics.A multi-strategy artificial bee colony(MS-ABC) algorithm is proposed for MSA, which is composed of multiple strategies, such as the Tent chaotic initialization population strategy, different neighborhood search strategies and tournament selection strategy.In the MSA-ABC algorithm, the Tent chaotic initialization population strategy is presented to diversify the initial individuals and to obtain good initial solutions.Then, the different neighborhood search strategies for different bee species are designed to balance the global exploration and the local exploitation.Moreover, the food source encoding method is used to adapt discreteness of MSA.The experimental results demonstrate that the proposed algorithm is more robust and can obtain better alignment quality and biological characteristics.