To analyze the persistence of the 35S promoter, nos terminator, and hpt, we buried the leaves and rootstocks of transgenic watermelons (Citrullus lanatus (Thunb.) Matsum. & Nakai) in 10 cm of soil. Qualitative and quantitative PCR analyses showed that the amount of transgenes in leaf samples was greatly decreased, by 70%, after 1 month, and only 2.5% remained after 2 months. No transgenes were detected in the leaves after 3 months. For buried rootstock samples, transgenes also degraded quickly, but a very small amount was still detectable up to 3 months later. In our investigation of possible gene transfer from decomposing transgenic watermelon to soil bacteria, only the 35S promoter was detected. However, further examination using colony dot hybridization tests indicated that such a transfer did not occur.