Base on the conserved Cyt b protein in prokaryotic and eukaryotic organisms and the phylogenetic analysis of Cyt b genes in organism from five different eukaryotic kingdom,we suggested that the eukaryotic Cyt b genes must have originated from an ancient prokaryotic genes in alphaproteobacteria . Despite common belief that mitochondrial house-keeping genes such as Cyt b is hardly to be transferred, our data indicate that the genes can be horizontally transferred to differrent mitochondria in distant species , and such event may have occured rather frequently. Therefore,the HGT events must be considered when evolutionary trees are constructed base on Cyt b genes. During evolution .mitochondrial genomes may gain intron sequences from other organelles or nuclei and the Cyt b intron-gaint event in eukaryotic organisms were occurred after the endosymbiosis of alphaproteobacteria in eukaryotes.