Xenocyprinae belonging to Cyprinidae, Teleostei, is a group of freshwater fishes mainly distributed in East-Asia. Not only are there many contradictions about its taxonomy at both genus and species level, but also little is know about its phylogeny. Furthermore, the relationship between Xenocyprininae and parasitic Hexamita is very special and interesting. In this study, the results have been obtained as the following: (1)A simple method for getting digoxigenin labelling probe of fish mtDNA has been established. (2)The RFLP analysis of mtDNA of 103 individuals belonging to Xenocyprinae being detected and the phylogram of the haplotypes was constructed by UPGMA and NJ. (3)The restrction maps of 27 haplotypes were constructed by double digested. The phylogenetic analysis by parsimony and neighbor-joining methods suggests that Xenocypris argentea and X. dividi are closely related and the relationship between Distoechodon hupeiensis and the genus Xenocypris is closer than that of between D. hupeiensis and D. tumirostris. The divergent time of Pseudobrama simoni was early in the subfamily. (4)The population genetic structure among four natural populations of X. argentea was analysed. The populations of Hubei and Hunan is rich in genetic diversity, but the populations of Fujian and Sichuan is poor. The relationship between Hubei-Hunan population and Fujian population is closer than that of between Hubei-Hunan and Sichuan. (5)A method of extracting large fragment DNA(1.2kb) from formalin-fixed specimens was developed. (6)The mitochondrial Cytb, ND4L, ND4, tRNA~(His), and tRNA~(ser) genes for 10 species from 4 genera of Xenocyprinae have been sequenced. A total of 2952 characters for each individuals were obtained. Our interpretation of the results from parsimony, distance and maximum likelihood based phylogenetic analysis suggests : X. argentea and X. dividi are closely related, and the relationship between D. hupeiensis and Xenocypris is closer than that of between D. hupeiensis and D. tumirostris. X. microlepis and X. fangi are sister groups., the ratio of mtDNA divergence in Xenocyprinae is seemly faster than that of other fishes having been reported and is nearly equal to that of mammals. (7)The mitochondrial Cytb genes for 22 genera from 11 subfamilies of Cyprinidae have been sequenced and the Cytb gene sequences of fishes in 9 orders have also been copied from Genebank. The results of phylogenetic analysis suggest : both the order Cypriniformes and the family Cypriniae could be regarded as monophyletic group. The family Cypriniae could be divided into two series, Leuciscini and Barbini. The subfamily Xenocyprinae may not be regarded as a monophyletic group. (8)The mitochondrial ND4L, ND4, tRNA~(His), and tRNA~(ser) genes for 15 species from 8 subfamilies have been sequenced. The results obtained in phylogenetic analysing of ND4L-ND4 gene sequences were the same as analysing Cytb gene, but the boostrap is higher at each branch. The results also show that as a phylogenetic maker ND4 gene may be better than Cytb gene. (9)The cladictic analysis using 24 characters of 17 species belonging to Hexamita parasitic in Xenocyprinae could not illustrated their phylogenetic relationships. (10)The phylogenetic tree of Xenocyprinae constructed by the fauna of parasitic Hexamita is the same as that of constructed by the method of molecular systematics. The results suggests that the fauna of parasite could reflect the relationship of host.