To screen and identify the genetic strains of genetically modified (GM) papayas in Shenzhen market for the sake of food safety risk assessment, and in order to provide scientific base for government regulation.Methods57Papayas were randomly collected from Shenzhen markets, detected by Real-time polymerase chain reaction (PCR) with CaMV35S promoter and NOS terminator for screening. The GM positive samples were identified with strain-specific primers and probes. ResultsIn 57papaya samples, the GM positive rate was 91.2% including 96.1% GMYK16-0-1strain and 3.9% Huanong-1strain respectively. Other strains were not detected. There was significant difference in the positive rates of transgenic papaya between supermarket and terminal market origin. No sample was labeled GM relevant.ConclusionNearly 90% GM papayas were the line that had not been approved by Chinese Ministry of Agriculture. Therefore the administrative departments should reinforce the supervision of GM papaya.