Abstract: Different subspecies or strains of the same species produce varied clinical manifestations. The clarifica-tion of parasite taxonomy is useful for the researches of their biology, epidemiology and control. DNA molecular markers have the advantages of high polymorphism, non-pleiotropy, and clear identifying alleles, etc. This paper summarizes the first generation （restriction fragment length polymorphism, random amplified polymorphic DNA）, second generation （simple sequence repeat-anchored PCR, inter-simple sequence repeat） and third generation （single nucleotide polymorphism） molecular marker techniques, and their application in taxonomic identification of parasites.

Key words: Parasite, Taxonomic identification, Molecular marker technique