Abstract: This article gives a brief introduction to several important issues in molecular systematics,that is,(1) advantages and limitations of molecular systematics;(2) relationship between molecular tree and species tree;(3) relationship between molecular clock and molecular systematics;(4) comparison of nucleotide sequence data and amino acid sequence data;(5) comparison of MP,NJ and ML method;(6) reliability of molecular tree.Two widely used softwares,PHYLIP and CLUSTAL V are briefly described.