Planctonema-like species consist of planktonic green algae and are found throughout the world. Their characteristic morphology, which includes short and slender filaments consisting of side-by-side or distant cylindrical cells enclosed in a fine and hyaline sheath, makes them easily distinguishable. To date, Planctonema lauterbornii was the only taxon accepted for this group. However, descriptions from different materials have revealed notable morphological differences, including the presence/absence of a pyrenoid, a mucilage sheath and an apical thickening of the cell wall. In this study, six strains of Planctonema-like species were identified and successfully cultured in the laboratory. We used a molecular approach to determine their taxonomic relationships and phylogenetic positions. The molecular analysis resolved them to at least three genera. The genus Planctonema was positioned in Trebouxiophyceae as an incertae sedis taxon that is closely related to Oocystaceae and was divided into two species. Planctonema gelatinosum was determined to be a new species with approximately twice the width and a thicker mucilage sheath, which differentiated it from the type species Planctonema lauterbornii. The genus Psephonema was reinstated based on 1.5-2 times length-width ratio than Planctonema and the big difference on the rbcL cpDNA gene marker and an intron insertion in the 18S rDNA. A new genus, Planctonemopsis, which represents the pyrenoid-present strains among the Planctonema-like species, was established. Planctonemopsis was positioned within Oocystaceae as a new clade and is distantly related to the other two genera. Taxonomic diversity was proven by distinctive morphological differences and phylogenetic divergence in the Planctonema-like group identified herein.