Biological network alignment is an important approach in the study of organisms’ structure, function and evolution. In this review, the recent studies in the field of biological network alignment are surveyed. First, a definition of biological network alignment is defined formally. Secondly, the methods for alignment are reviewed and described into three categories according to their mathematical properties. Some models and algorithms in every category are analyzed comprehensively and comparably. Next, tools for alignment are listed and analyzed. In the end, some applications and key problems in the field are highlighted, as well as the future progress of biological network alignment.