The genus Chroomonas is a group of blue-green colored cryptomonads. This study describes two freshwater Chroomonas species for the first time in South Korea: Chroomonas nordstedtii Hansgirg and Chroomonas coerulea (Geitler) Skuja. We examined the morphology and ultrastructure of these species by light microscopy, scanning electron microscopy, and transmission electron microscopy. These two Chroomonas species were blue-green colored and ovate to oval-shaped. Chroomonas nordstedtii was characterized by two Maupas ovals with hexagonal periplast plates, whereas C. coerulea was characterized by one eyespot with rectangular periplast plates. A molecular phylogeny with data from nuclear SSU rRNA and chloroplast rbcL genes revealed that Korean C. nordstedtii formed a distinct clade with NIES-708, NIES-1004 from Japan, and UTEX 2779 from Colorado, USA, while C. coerulea formed a clade with ACOI 1366 from Portugal.