Abstract: It used mal d 4.02 gene for apple allergen and MA023a gene for peach microsatellite mark as specific primers of apple and peach, respectively. The chloroplast AccD gene of highly conserved plant was used as endogenous gene. Species-specificity of apple and peach fruit juice was identified by PCR technology. In the results, the specific PCR detection method could accurately identify apple and peach species. The minimum detection limit of the specific PCR method for apple and peach fruit was 5ng /mL and 10ng /μL.This method could qualitative identify apple and peach juice quickly and accurately.