Hot branding has been used for many years by researchers to identify seals from a long distance. In livestock, cold branding has been proposed as an alternative because it is thought to be less painful. The purpose of this study was to compare the healing process of hot and cold brands applied to harbour seal pups (Phoca vitulina). A total of 306 animals was branded with a unique set of four characters: three applied for 3–5 s with an iron heated to 500°C, and one applied for either 10 or 20 s with an iron frozen to –175°C. At three subsequent times over 10 weeks, 43, 41 and 51 animals, respectively, were recaptured, the macroscopic appearance of their brands recorded, and biopsies taken for microscopic examination. Cold brands had a faster healing rate than hot brands. However, they resulted in less destruction of hair follicles, and cold brands applied for 20 s caused more depigmentation. Regrowth of hair follicles could subsequently obscure brands, while depigmentation reduces the contrast between the brand and the surrounding fur. Cold brands applied for 20 s also caused more extensive deep vascular damage, which subsequently may have resulted in deeper wounds in some of these brands. Yet, macroscopically, other cold brands, or portions thereof, were almost invisible. On the basis of this short-term study, the technique of cold branding that we used in harbour seals does not appear to be as reliable as that of hot branding to provide permanent legible brands.