Abstract: Pairwise alignment is one of the major problems in bioinformatics，the solution to which is to devise pertinent and efficient algorithms to discern the most similar matching between two sequences of DNA or protein through some certain algorithms，and then to establish whether the two enjoy the quality of the same source.In the careful examination of the practical importance of pairwise alignment，the article suggests and illustrates that the best alignment may not necessarily reflect the actual process of evolution.Emphasis lays upon the most important one——general alignment algorithm（Smith Waterman’s algorithm）.Finally，the paper puts forward a way by which all the passed routes can be recorded with arrays in the process of alignment，which，by means of recursion，is able to be transferred to a certain use so that the most similar result of alignment can be located.