Abstract: During the tomato fruit color development, transcription factor may play important roles. From an introgression line population derived from tomato wild species Solanum lycopersicoides, we found a yellow-fruit mutant line which was different from redfruit patent. We took red-fruit parent tomato and yellow-fruit mutant as genetic materials to study the gene expression profiles of MYB transcription factor by digital gene expression sequencing and RT-PCR. As results, we screened out many MYB transcription factors related to tomato fruit color and differential expressed in yellow-fruit and red-fruit tomato, and verified one of them by RT-PCR.