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Background  Water-soluble anthocyanin pigments are important ingredients in health-improving supplements and valuable for the food industry. Although great attention has been paid to the breeding and production of crops containing high levels of anthocyanin, genetic variation in red or purple cabbages ( Brassica oleracea var. capitata F. rubra ) has not yet been characterized at the molecular level. In this study, we identified the mechanism responsible for the establishment of purple color in cabbages.    Results   BoMYBL2–1  is one of the regulatory genes in the anthocyanin biosynthesis pathway in cabbages. It is a repressor whose expression is inversely correlated to anthocyanin synthesis and is not detectable in purple cabbages. Sequence analysis of purple cabbages revealed that most lacked  BoMYBL2–1  coding sequences, although a few had a substitution in the region of the promoter 347 bp upstream of the gene that was associated with an absence of  BoMYBL2–1  expression. Lack of transcriptional activity of the substitution-containing promoter was confirmed using transgenic  Arabidopsis  plants transformed with promoter::GUS fusion constructs. The finding that the defect in  BoMYBL2–1  expression was solely responsible for purple coloration in cabbages was further demonstrated using genomic PCR and RT-PCR analyses of many other structural and regulatory genes in anthocyanin biosynthesis. Molecular markers for purple cabbages were developed and validated using 69 cabbage lines.    Conclusion  Expression of  BoMYBL2–1  was inversely correlated to anthocyanin content, and purple color in cabbages resulted from a loss of  BoMYBL2–1  expression, caused by either the promoter substitution or deletion of the gene. This is the first report of molecular markers that distinguish purple cabbages. Such markers will be useful for the production of intraspecific and interspecific hybrids for functional foods, and for industrial purposes requiring high anthocyanin content.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1290-9) contains supplementary material, which is available to authorized users.

Purple Brassica oleracea var. capitata F. rubra is due to the loss of BoMYBL2–1 expression