The molecular marker technology of fruit color traits for the selection of colored bell peppers includes two molecular markers: (1) sequence characterized amplified region marker (SCAR marker); (2) cutting amplified multi-type sequence marker ( cleaved amplified polymorphic sequences referred to as CAPS marker). The technology can provide fruit color genotype analysis of color sweet pepper breeding parents, or can be used for color pepper selection of specific fruit colors. This technology is applied to the verification of seedling stage, which can save the human and material cost of fruit color selection. It is also helpful for the exploration of the color pepper germplasm of a specific fruit color, which can promote the breeding of a new variety of color pepper.