Mature zygotes of the cosmopolitan snow alga Chloromonas nivalis (Chodat) Hoham & Mullet [=Scotiella nivalis (Chodat) Fritsch] collected from Mt. Gassan, Yamagata Prefecture, were examined by scanning electron microscopy (SEM) and single-cell sequencing of the large subunit of Rubisco (rbcL) genes. I-lie present SEM demonstrated that Japanese samples have at least two types of flanges on the zygote wall (straight and sigmate). Although these types fell within the morphological variability of C nivalis as reported previously, at least two types of rbcL (large Subunit of Rubisco) gene sequences were detected by Using the single-cell sequencing. Although the information of the rh(L genes were limited (340-400 bp), the present phylogenetic analyses revealed that these two Japanese types and C. nivalis originating front North America belong to the lineage composed of Chloromonas snow taxa. Thus, C. nivalis might involve multiple cryptic species of Chloromonas. Further ovservations of other stages of life cycle and more detailed phylogenetic analysis are needed to reveal the correct taxonomic identifications of C. nivalis.