Accurate uses of key components and right media during tissue cultures are vital for a particular process and repeatable outcome in plant transformation. If additional components, as indicators, can be added into media, it could avoid some of the issues, such as adding a wrong component or misrecognition of a right medium. We tested to add a specific pigment into a set of media sharing a key common element, such as a selection agent, so that all media containing the same selection agent appeared in a certain coloration to provide a convenient marker for all people involved in the process of transformation. The effect of four color pigments on tissue cultures of corn, rice, and soybean was evaluated in this study. The results show pigment brilliant blue, Pyla-Cert green, and mixture purple neither impacted soybean cotyledon growth nor callus formation and shoot regenerations of corn and rice. In soybean hair root transformation, addition of pigment blue, green, erythrosine red and mixture purple into the selection media did not reduce its transformation frequency and copy number. However, erythrosine red resulted in lower callus formation rates and low regeneration rates among rice and corn. Further, fresh weight and dry weight of soybean cultures were increased on the media containing erythrosine red. Therefore, we recommend using pigment brilliant blue, Pyla-Cert green and mixture purple as indicators for selection agents in the transformation process of maize, soybean, and rice to prevent misuse of wrong components or wrong media.