Different subspecies or strains of the same species produce varied clinical manifestations. The clarification 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.