Abstract The mitochondrial functional protein alternative oxidase （AOX）genes were took as the research target in this experiment, the genes of all strains that preserved in our lab were amplfied and sequenced. Then compared the sequences with other related sequences downloaded from GenBank by using Clustal X1.81.Three types of phylogenetic analysis were used on the aligned sequences to assess relationships among isolates, the distance-based neighbor-joining(NJ) analysis, parsimony(MP) analysis and Maximum Likelihood(ML). NJ tree and MP trees were constructed with the program PAUP, while ML tree was made by using PUZZLE Version 4.1.Then determined phylogentic realationship of different Cryptospoiridum genus or genotype and contrasted those phylogentic trees with that of drawed by 18SrRNA and HSP70 gene sequence, and determined whether the AOX gene is suitable for phylogentic analysis of Cryptosporidim or not. In those phylogentic trees Cryptosporidium species formed two group, one group contained C.baileyi and C.meleagridis , the other group contained C.hominis、C.suis、C.parvum cattle genotype and C.parvum mouse genotype. The sequence identity of different Cryptosporidium species ranges from 91.8% to 99.6%. The results showed that the AOX gene is equally suitable for the phylogentic analysis of Cryptosporidim .
