Pseudendoclonium was established in 1900 by N. Wille to include a crust-forming green microalga occurring near the high water line on jetties in Drobak, Norway. Ordinal and familial affiliation of the genus have remained uncertain due to a lack of distinguishing morphological characteristics and because molecular phylogenetic data have not been generated for the type species. Ribosomal SSU rDNA sequence data for Pseudendoclonium submarinum, the type species, are presented. Phylogenetic analysis of these data place Pseudendoclonium within the Ulvales. SSU rDNA sequence data from three additional species, Pseudendoclonium basiliense, Pseudendoclonium akinetum and Pseudendoclonium fucicola are included in the analyses and clearly support the hypothesis that Pseudendoclonium is polyphyletic. Based on the sequence data, P. submarinum and P. fucicola share ulvalean lineage, but these algae are not congeneric and P. fucicola must be removed from Pseudendoclonium. Sequence data support the classification of P. basiliense and P. akinetum as distinct species of a single genus. The close affiliation of these two species with Ulothrix and other Ulotrichalean genera, however, reveals their ordinal separation from P. submarinum. P. basiliense and P. akinetum must also be removed from Pseudendoclonium and require generic reassignment within the Ulotrichales.

The genus Stigeoclonium is taxonomically very problematic. The relationships between species of this genus are very little known. There are only a few studies that deal with only morphological revision of the genus Stigeoclonium. Hovewer, up to now no phylogenetic analysis of this genus exists. This study summarizes the knowledge about the genus Stigeoclonim in the Czech Republic and shows the first phylogenetic analysis of this genus.