A eukaryotic marine microalga was isolated from Jungmun Saekdal Beach, Jeju Island, Korea and an integrated approach, including molecular phylogeny and morphology, was used to determine its taxonomical status. Molecular phylogenetic evidence inferred from the small subunit (SSU) 18S rRNA sequence and internal transcribed spacer (ITS) secondary structure analysis clearly showed that the isolate belonged to the recently described species, Jaagichlorella roystonensis. Distinctive morphological keys of the species were also observed by light microscopy and scanning/ transmission electron microscopy (S/TEM). In this study, a Korean marine J. roystonensis species was described for the first time and was subsequently added to the national culture collections in Korea.