Sea squirts were collected from shallow waters of 0.5–5.0 m depth at 27 harbors or ports in Korea: 14 harbors in the East Sea, 10 harbors in the Korea Strait, and three harbors in the Yellow Sea. Ciona intestinalis was identified as an introduced alien species and was compared with the Asian native C. savignyi, which was first reported in Korea. Four distinct morphological differences are recognized between these two species: 1) shape of pigment spots on branchial and atrial siphons, 2) flecks of body, 3) color or shape of the tip of the vas deferens, and 4) thickness and transparency of the body wall. Phylogenetic relationships of these species are examined through molecular analysis based on 720 bp of mtCOI gene sequences. Korean C. intestinalis belong to Type A.