Species of the diatom genus Chaetoceros with special intercalary setae are uncommon. For this study, we collected Chaetoceros species from August 2008 to September 2009 in Korean coastal waters and examined the ultra structures of the Chaetoceros species C. coarctatus, C. compressus var. hirtisetus, C. contortus, C. diversus, and C. messanensis, using light and scanning electron microscopy. C. coarctatus, in the subgenus Phaeoceros, showed longer and stronger spines than those found in other species. C. coarctatus and C. diversus had special intercalary setae with spines in straight arrangements, whereas C. compressus var. hirtisetus, C. contortus, and C. messanensis had special intercalary setae with spines arranged in spirals. The setae of C. coarctatus had spines that were robust toward the tips and, overall, longer and stronger than were those of other species. C. coarctatus and C. diversus were straight, and C. compressus var. hirtisetus, C. contortus, and C. messanensis spiraled. C. messanensis had two types of special intercalary setae, both forked: 1 with spines in spirals and 1 lacking spines. We did not find spines on the anterior part of divergent point of the special intercalary setae of C. messanensis. Foramina shapes of these 5 Chaetoceros species varied as follows: very small or no foramina in C. coarctatus, relatively wide and slightly centrally constricted foramina in C. compressus var. hirtisetus and C. contortus, quite narrowly slitted or no foramina in C. diversus, and lanceolate or hexagonal foramina in C. messanensis. We found rimoportula in both intercalary and terminal valves of C. coarctatus, but C. compressus var. hirtisetus, C. contortus, C. diversus, and C. messanensis only had rimoportula in terminal valves. In addition, C. compressus var. hirtisetus and C. contortus were new to Korean coastal waters.