There are 6 methods, pyrolysis, high-salt low-pH, isopropyl alcohol, CTAB, SDS or GuSCN, used in the extraction of milk powder genomic DNA for the molecular marker analysis of high quality and sufficient samples. To find out the better method of them, the effects of different methods were compared by detecting the DNA by optical density, agarosegel electrophoresis and polymerase chain reaction (PCR). The results showed that the genomic DNA extracted by all methods except for isopropyl alcohol and SDS method could be used in PCR reaction. Meanwhile, the better DNA concentration and purity could be gained by different methods in the order of pyrolysis, GuSCN, High-salt low-pH, CTAB. These methods are simply to operate, fast to gain results, and suitable for the extraction of total DNA from milk powder.