Background: Anthocyanins represent one of the most abundant coloration factors found in plants. Biological functions of anthocyanins range from reproduction to protection against biotic and abiotic stressors. Owing to a clearly visible phenotype of mutants, the anthocyanin biosynthesis and its sophisticated regulation have been studied in numerous plant species. Genes encoding the anthocyanin biosynthesis enzymes are regulated by a transcription factor complex comprising MYB, bHLH and WD40 proteins. Results: A systematic comparison of anthocyanin-pigmented vs. non-pigmented varieties across flowering plant species was performed. Literature was screened for cases in which causal genes were previously identified. Transcriptomic data sets were processed to determine the genes most likely to be responsible for color variation based on their expression pattern. The contribution of different structural and regulatory genes to the pigmentation differences was quantified. Gene expression differences concerning transcription factors are by far the most frequent explanation for pigmentation differences observed between two varieties of the same species. Among the transcription factors in the analyzed cases, MYB genes are substantially more likely to explain pigmentation differences than bHLH or WD40 genes. Conclusions: These findings support previous assumptions about the plasticity of transcriptional regulation and its importance for the evolution of novel coloration phenotypes. The particular significance of MYBs and their apparent dominant role in the specificity of the MBW complex are underlined by our findings.