The Japanese shrimp industry depends on importing shrimp from other countries. However, little information is available on mercury speciation and selenium (Se) concentrations in commercial shrimp available in Japan. The present study determined the concentrations of total mercury (T-Hg), methylmercury (MeHg), and Se in the muscles (wet weight) of imported and domestic commercial shrimp from Kumamoto and Kagoshima prefectures to obtain information for assessing the risk of MeHg exposure. The median concentrations of T-Hg, MeHg and Se in shrimp imported from three different countries were, respectively: black tiger shrimp (n = 18), 15.8, 14.4, and 415 ng/g; Vannamei shrimp (n = 25), 11.4, 11.2, and 292 ng/g; and white shrimp (n = 26), 26.8, 26.1, and 396 ng/g. There were significant differences in T-Hg and MeHg concentrations between shrimp imported from different countries. The median concentrations of T-Hg, MeHg and Se in shrimp of Japanese origin were, respectively: Shiba shrimp (n = 10), 15.9, 15.0, and 270 ng/g; Kuruma shrimp (n = 10), 79.9, 75.9, and 390 ng/g; and Ashiaka shrimp (n = 10), 36.1, 34.1, and 303 ng/g. The percentages of MeHg in T-Hg were between 90% and 99%, with MeHg levels in the imported and domestic commercial shrimp lower than the Japanese regulation of 300 ng/g for fish. The mean Se/T-Hg molar ratios (16-160) were comparatively higher than those previously reported in fish. Overall, this survey suggests that shrimp commercially available in Japan will not pose a particularly high risk regarding MeHg exposure to consumers.