The complete sequence of the cucumber mosaic virus (CMV) satellite RNA (satRNA) gene that was controlled by the cauliflower mosaic virus (CaMV) 35S promoter (P-35S) and the Agrobacterium nopaline synthase terminator (T-nos) was first identified in an unapproved genetically modified (GM) tomato (Solanum lycopersicum L.), and a duplex polymerase chain reaction (PCR) method was developed based on the CMV satRNA nucleotide sequence. To detect the unapproved GM tomato, the metallocarboxypeptidase inhibitor (Mcpi) gene was selected as an endogenous reference gene for tomato and was validated using 13 different crops. The primer pair PTD-F/R was designed to amplify the junction sequences between the 35S promoter and CMV satRNA gene introduced in the unapproved GM tomato, and its specificity was also validated using several different GM events. The detection limit of the duplex PCR method is approximately 1 copy. Using the duplex PCR method, 35 processed tomato foods and 13 tomato seeds were analyzed. Of these samples, 2 GM tomato seeds were identified using the duplex PCR method. The results indicate that this duplex PCR method could be useful for detecting the unapproved GM tomato.