Abstract: The aim of this study was to investigate the difference of class Ⅲ peroxidases (Prxs) genes between Saccharum officinarum and Saccharum arundinaceum and explore the genetic basis of the functional differences of Prxs genes in these two species by cloning and analyzing their Prxs gene. A Sorghum bicolor Prxs gene was used as probe, by using the homologous clonal strategy, Prxs genes were cloned from Saccharum officinarum and Saccharum arundinaceum. In this study, four Prxs genes cDNA were obtained, both of the two Prxs genes cDNA length in Saccharum arundinaceum were 1083 bp, there was only one different site between them, another two Saccharum officinarum Prxs genes cDNA length were 1084 bp, which had eleven bases difference. The four cloned genes had a 996 bp open reading frame, encoding 331 amino acid. The protein conservative structural domain analysis showed that all of the four cloned genes had typical well-conserved amino-acid residues of Prxs, and they were the aimed genes. The phylogeny analysis indicated that the cloned genes had high similarity with homologous genes in Sorghum bicolor, zea maize and oryza sativa, also had relationship to the dicotyledon plants, or even to some gymnosperms, and the similarity degree of amino acid sequences were consistent with species divergence, which provided an evidence for plant classification. Four Prxs genes were cloned from Saccharum officinarum and Saccharum arundinaceum in this study, it provided a reference for further study in distinguishing the functional difference among different plants.