Genetically modified (GM) tomatoes have been approved for commercialization in many countries since the first GM tomato FLAVR AVAR was permitted for planting in 1994. In China, GM tomato BIOSCIEN with a character of long shelf life was the first GM plant approved for commercialization in 1996. To meet the requirement of GM tomatoes labeling policy that has been actualized in China since 2001, the screening and construct specific PCR detection for detecting the universal elements transformed into tomato, such as Cauli flower mosaic virus 35 S(CaMV35S ) promoter and the nopaline synthase ( NOS ) terminator of Agrobacterium tumefaciens , and the specific inserted heterologous DNA sequence between CaMV35s promoter and anti sense ethylene forming enzyme (EFE ) gene were set up, respectively. To make the detection methods normative, a novel single copy tomato gene LAT52 was also used as an endogenous reference gene in the PCR detection systems. The limit of detection (LOD) of screening and construct specific detection for BIOSCIEN was 68 haploid genome copies in conventional qualitative PCR detection, and 3 copies in TaqMan real time PCR detection. The limit of quantification (LOQ) of screening quantitative PCR assay for BIOSCIEN was 3 copies and 25 copies for construct specific quantitative PCR. Two samples with known BIOSCIEN tomato contents were detected using the established conventional and real time PCR systems,and the results indicated that the established BIOSCIEN screening and construct specific PCR detection systems were reliable, sensitive, and accurate.