Tomato fruit color, which is the most visible characteristic among the other fruit traits, is considered to have a substantial influence on consumers. The pink-colored tomatoes with high soluble solids content are considerably preferred especially in Asia compared to the other colors. Generally the pink fruit trait of tomatoes is easily determined by visual examination of intact fruit, however, it is technically determined by the characteristic of the fruit peel. The pink trait is regulated by variations of the SlMYB12(y) gene located on chromosome 1, which controls the accumulation of the naringenin chalcone, which comprises a large proportion of flavonoids. In this study, we developed a derived Cleaved Amplified Polymorphic Sequences (dCAPS) marker and a sequence characterized amplified regions (SCAR) marker in order to discriminate of pink/non-pinktomatoes in the domestic breeding lines. Quantitative RT-PCR analysis indicated that the SlMYB gene is highly expressed in non-pink fruit peel, whereas the expression is significantly lowered in the pink fruit peel. These gene based markers are expected to enhance the efficiency and accuracy of selection pink-tomatoes in tomato breeding programs.