The distribution and incidence of melanoma vary among different races and ethnic groups. This study aimed to investigate the characteristics of cutaneous melanoma, mucosal melanoma, uveal melanoma, and melanoma of unknown primary (MUP) origin in a Japanese population. We studied these four types of melanoma in patients registered in Hospital Based Cancer Registries in Japan from 2011 to 2013. A total of 5566 patients with melanoma were identified. The distribution of sex, age, primary site, and clinical stage was analyzed. The number of patients, proportion in comparison with all melanoma cases, and crude incidence rate per 100 000 person-year of each melanoma type were 4481, 80.5%, and 1.24 in invasive cutaneous; 821, 14.8%, and 0.32 in mucosal; 163, 2.9%, and 0.064 in uveal; and 101, 1.8%, and 0.039 in MUP origin, respectively. Including the patients with in-situ cutaneous melanoma and stage unknown cutaneous melanoma, the crude incidence rate of cutaneous melanoma increased at 1.75. Almost half of the cutaneous melanomas were located in the lower limb. Cutaneous melanoma was the most common, but less frequent than that in western countries. Mucosal melanoma was quite rare, but its proportion and crude incidence rate were higher than those in western countries. Uveal melanoma was particularly rare, and its crude incidence rate was lower than that in western countries. MUP origin was also particularly rare, but it had almost the same incidence rate as that in other countries. Melanoma in Japan was heterogeneous among the four melanoma types and shares some attributes with that in western countries.