Analyses of partial small subunit (SSU) and large subunit (LSU) rRNA genes of Rhizoclonium-like filamentous green algae, collected from brackish waters in Japan, revealed the existence of five genetically distinct species. Four species (Rhizoclonium spp. 1-4) were closely related to Rhizoclonium hieroglyphicum. The phylogenetic position of the Rhizoclonium-like sp. 5 remained largely unresolved, although LSU analyses suggested a relationship with Chaetomorpha ligustica. Rhizoclonium spp. 1 and 4 were identified as Rhizoclonium riparium and Rhizoclonium lubricum, respectively. Rhizoclonium spp. 2 and 3 were morphologically distinguishable from other Rhizoclonium species and minute Chaetomorpha species. Rhizoclonium sp. 2 exhibited a characteristically small L/D (cell length/cell diameter) ratio and large number of nuclei (3-7 per cell), while Rhizoclonium sp. 3 was characterized by unique spindle or band-like, densely arranged chloroplasts
therefore, we described them as new species, Rhizoclonium breve and Rhizoclonium confertum. Rhizoclonium-like sp. 5 was characterized by perforated chloroplasts and polypyramidal pyrenoids and was clearly distinct from known Rhizoclonium or Chaetomorpha species. Based on the phylogenetic position and morphological features of Rhizoclonium-like sp. 5, we described it as a new species of Chaetomorpha, Chaetomorpha tokyoensis.