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A fast and efficient recognition method of transgenic lines will greatly improve detection efficiency and reduce cost. In this study, we successfully identified the transgenic soybean plants by the color. We isolated a GmW1 gene encoding a flavonoid 3050-hydroxylase from a soybean cultivar ZH42 (purple flower). We found that purple flowers occurred in the overexpression lines in the Jack and Williams 82 backgrounds (white flower). All plants with purple flowers were positive, and this trait seems stably inherited in the offspring. We have also obtained the editing plants, which were classified into three types according to the different flower colors appeared. We analyzed the phenotype and the homozygous types of the T1 mutants. We also found that a correspondence between flower color and stem color. This study provides a visible color reporter on soybean transformation. It can be quickly and early to identify the transgenic soybean plants by stem color of seedlings, which substantially reduces the amount of labor and cost. [ABSTRACT FROM AUTHOR]