Abstract: In order to find suitable methods for total DNA extraction from seeds and flesh of transgenic apple, Modified CTAB method, SDS method, and High Salt low pH SDS method were applied to transgenic CpTI gene Gala apple. The results showed that reasonable quality DNA could be obtained from seeds by using all three methods applied in this experiment, but the yield of DNA varied from each other. The using of the modified CTAB method generated the highest yield of 0.221 mg?g-1 FW, and the SDS method and High Salt low pH SDS method had the lower yield of 0.053 mg?g-1 FW and 0.034 mg?g-1 FW, respectively. For the DNA extraction from flesh, the using of SDS method had the best result in terms of the DNA quality and yield with the value of A260/ A280 at 1.808 and yield of 0.012 mg?g-1 FW, and the rest of the two methods did not give good result in terms of the DNA quality. It could be concluded that the modified CTAB method was suitable for DNA extraction from transgenic apple seeds and the SDS method was suitable for that from transgenic apple flesh in taking into account both the quality and yield of DNA.