Abstract: The taxonomic status of the genera Lignincola and Nais was re-evaluated by phylogenetic analysis of the partial large subunit ribosomal DNA sequence. Both Lignincola and Nais are inferred to be polyphyletic genera. Lignincola laevis and L. longirostris are phylogenetically related taxa but they are not monophyletic. Nais inornata, the type species of the genus, has a close relationship with Aniptodera (A. chesapeakensis) while N. glitra forms a well-supported clade with Halosarpheia abonnis and H. ratnagiriensis. Neptunella gen. nov. is introduced to accommodate L. longirostris and Saagaromyces gen. nov. to accommodate H. abonnis, H. ratnagiriensis and N. glitra.