Skin color of red potatoes is due to accumulation of anthocyanins in the tuber periderm, a protective tissue that replaces the epidermis at an early stage of tuber development. The periderm consists of external layers of suberized phellem cells making up the skin, and internal layers of parenchyma‐like phelloderm cells. Red pigmentation is an important marketing factor for red‐skinned potatoes. However, injuries to the tuber surface, which are common in the potato industry, result in the development of a wound periderm that is devoid of the characteristic red coloration. To study the reason for these differences in anthocyanin accumulation, the expression level of anthocyanin biosynthesis genes and regulators was monitored in native and wound periderm using microarray analysis and quantitative polymerase chain reaction. We found significantly higher expression of the anthocyanin pathway in the phelloderm cells compared with the skin and tuber‐flesh samples. However, in wound periderm, the anthocyanin pathway was strongly downregulated relative to the native periderm. This was true for two developmental stages of the native periderm – ‘immature’, when the skin is prone to skinning injuries, and ‘mature’, following skin set – suggesting that anthocyanin synthesis continues postharvest. Wound‐induced expression of steroidal glycoalkaloid glycosyltransferases, suberin‐related 3‐ketoacyl‐CoA synthase and actin indicated that downregulation of the anthocyanin‐specific pathway does not reflect global repression of the wound‐periderm transcriptome. Loss of pigmentation may result from reduced expression of the Myb–bHLH–WD40 anthocyanin regulatory complex – a possible candidate might be the bHLH transcription factor JAF13.