Eighteen populations of Melilotus alba and Melilotus officinalis were used to study the genetic diversity by ITS and trnL-trnF sequences.The results showed as followings:(1)The aligned length of trnL-trnF sequences was 459 bp and there were 6 parsimonious informative sites,6 variable sites and 33.1% G+C content.The aligned length of ITS sequence was 714 bp and there were 4 parsimonious informative sites,6 variable sites and 48.9% G+C content.(2)All Melilotus L.populations could be divided into two groups in the phylogenetic tree of trnL-trnF,which showed that trnL-trnF sequence had the identify ability in the molecular phylogeny study of Melilotus L..(3)The genetic diversity of M.officinalis was higher than that of M.alba in both sequences by analyzing haplotypes and nucleotide diversity.