Abstract: Abstract: Based on the protein databases of several model species, this study developed a new method of the Genome-wide prediction for the target genes, using Hidden Markov model by Perl programming. The advantages of this method are high throughput, high quality and easy prediction, especially in the case of multi-domains proteins families. By this method, we predicted the PPR and TPR proteins families in whole genome of several model species. There were 536 PPR proteins and 199 TPR proteins in Oryza sativa ssp. japonica, 519 PPR proteins and 177 TPR proteins in Oryza sativa L. ssp. indica, 735 PPR proteins and 292 TPR proteins in Arabidopsis thaliana, 6 PPR proteins and 32 TPR proteins in Cyanidioschyzon merolae. Synechococcus and Thermophilic archaebacterium did not have PPR proteins. By contrast, 10 TPR proteins were found in Synechococcus and 4 TPR proteins were found in Thermophilic archaebacterium. Moreover, of these results, some further bioinformatics analyses were conducted