A eukaryotic microalga was isolated from seawater in Janghang Harbor, Korea and its morphological, molecular, and physiological characteristics were investigated. Due to its simple morphology, no distinctive characters were found by morphological observation, such as light microscope or scanning/transmission electron microscopy (S/ TEM). However, molecular phylogenetic evidence inferred from the concatenated small subunit (SSU) 18S rRNA and internal transcribed spacer (ITS) sequence data indicated that the isolate belonged to the newly described Micractinium singularis. Furthermore, it was clustered with Antarctic Micractinium strains and it also showed a psychrotolerant property, surviving at temperatures as low as 5°C. However, its optimal growth temperatures range from 15°C to 25°C, indicating that this microalga is a mesophile. Additionally, gas chromatography-mass spectrometry (GC/MS) analysis showed that the isolate was rich in nutritionally important omega-3 polyunsaturated fatty acid, and high-performance liquid chromatography analysis (HPLC) revealed that the high-value antioxidant lutein was biosynthesized as an accessory pigment by this microalga, with glucose as the major monosaccharide. Therefore, in this study, a Korean marine M. singularis species was discovered, characterized, and described. It was subsequently added to the national culture collections.