Objective To investigate the effects of different heating methods on the degradation of carp DNA and to compare different DNA extraction methods. Methods The dorsal muscle of carp was boiled for 1, 2 and 3 h by electromagnetic oven or microwave oven. Genomic DNA of carp meat was extracted by four different methods (phenol/chloroform extraction, Wizard? commercial Kit, Mag-Bind DNA Kit and spin column). The length of DNAs before and after heat treatment was compared by agarose gel electrophoresis. The contents of ?-actin in tested DNA samples were determined by Real-time PCR assays. Results The contents of β-actin DNA after heating for 1, 2 and 3 h in electromagnetic oven were 143 309, 441 350 and 256 994 copy/μl and those in microwave oven were 269 121, 267 371 and 134 650 copy/μl respectively. The contents of raw carp β-actin DNA was 1 070 213 copy/μl, which were decreased significantly after being heated. However, the contents of β-actin DNA would be no significant change with extended heating time. The contents of DNA extracted by phenol/chloroform or Wizard^? commercial Kit (718 945 and 737 946 copy/μl respectively) were higher than that by spin column and Mag-Bind DNA Kit (26 751 and 2 934 copy/μl respectively). Conclusions DNA could be degraded by heating for more than 1 h. Therefore, the target fragments of DNA in food selected for DNA detection should be shorter. As for the extraction methods, the contents of DNA extracted by phenol/chloroform ion and Wizard^? commercial Kit were higher than that by spin column and Mag-Bind DNA Kit.