Frataxin protein is a component of Fe-S clusters and closely related to metabolism of mitochondria. We identified an integrity mitochondrial protein frataxin gene (Nbfra), analyzed its phylogenetic relationship, and confirmed the transcriptase activity of Nbfra in N. bombycis.We analyzed the sequence of the second structure, gene location in genome and construction of NJ phylogenetic tree through various bioinformatics software. We constructed recombinant vector pGEX-4T-1-Nbfra, expressed the 36.5kDa recombinant protein in E. coli BL21 (DE3), and then used the protein as antigen to produce its polyantibody in mice.Nbfra was lack of targeting signal into mitochondria and part of alpha helices in functional domain, and had a synteny character between N. bombycis and E. cuniculi. Phylogenetic trees of Nbfra suggested that the evolutionary position of microsporidia was closely related to that of higher eukaryote, rather than that of other protozoa. The result of western blot suggested the expression and transcription of Nbfra gene in N. bombycis.Our results offered the new evidence to analysis the conservation of Nbfra and evolutionary position of N. bombycis, and would support the hypothesis of mitosome in microsporidia.