Abstract: The problem of“tied trees”has been noticed in the traditional NJ(Neighbor Joining)method, which may produce more than one phylogenectic tree from a single data set,depending on the order of data entry.To solve this problem,this paper presented an improved NJ algorithm.Being different from the traditional NJ algorithm,the improved NJ repeatedly merged multiple groups into one by rate-corrected distance until only one group remained.The author shows in theory and application that the improved algorithm can always produce a unique phylogenetic tree,which is the same as the original NJ tree without considering the order of branches in cases that they are actually bifurcating.Thus it may produce a multifurcating tree with a unique topology,even if the original NJ trees are tied.