Abstract: The aim of this paper is to acquire a new marker gene of banana under the infection of Foc TR4. A peroxidase gene was identified by randomly sequencing from cDNA library obtained from banana roots. This gene was called MaPOD1 (GenBank accession number is KC478598). The cDNA sequence obtained by amplifying was consistent with plasmid sequence, indicated that this gene was full-length cDNA of banana POD gene, which contained an open reading frame of 948 bp encoding a protein of 328 amino acids. Through protein sequence homologous compare, it was found that the gene contained peroxidase active site and heme binding site structure. Semi quantitative RT-PCR demonstrated that the expression of MaPOD1 was higher in banana roots and pseudostems while lower in rhizomes. In resistant and susceptible varieties of banana after inoculation Foc TR4, the expression of MaPOD1 was upregulated, but in resistant varieties the time point of MaPOD1, compared to control, increased higher than that in susceptible varieties at time points, indicated that this gene played an important role in banana resistance. The expression of this gene had the same trend with enzymatic activity change, and gene expression lagged after enzyme activity change. MaPOD1 could be a new marker gene under the infection of Foc TR4.