Transgenic plants that over express virus coat protein genes have attracted particular interest from researchers, by virtue of their tolerance to virus infection. The transgenic watermelon rootstock analyzed in this study was established by introducing CGMMV coat protein (cp) under the control of CaMV 35S promoter and NOS terminator (Park et al., (2005) Plant Cell Rep. 24: 350-6). The primary objective of this study was to determine the copy number and integration site of the transgene element, in order to develop detection techniques required for monitoring of the transgenic watermelon rootstock. The Southern blot analysis indicated that a single copy of CGMMV-cp gene was inserted into the genome of transgenic watermelon rootstock. We also identified the genomic sequences flanking the integration site of the transgene by inverse PCR analysis. In an effort to find a sequence usable as an internal positive control for the screening of the watermelon and watermelon rootstock, we found that the Sat and DIP-1 genes appears as one copy within their genomes and is watermelon rootstock- and watermelon-specific. The information of the integrated site and the internal positive control sequence was used to establish a new event-specific PCR-based detection method. In addition, mRNA and protein expression level of the transgene in the transgenic watermelon rootstock and grafted watermelon were investigated. The expression of both mRNA and protein of CGMMV-CP was not detected in the transgenic watermelon rootstocks and watermelons, suggesting that the movement of transgene products from transgenic rootstock to watermelon does not occur at our detection level.