Chlamydomyxa labyrinthuloides is a heterokont alga known since the last century. It lives on Sphagnum and other water plants as aplanospores or plasmodia. We have investigated the taxonomic position of Chlamydomyxa labyrinthuloides by combining results from morphological studies, pigment analyses and a molecular phylogenetic analysis of the small subunit (SSU) rRNA gene. Chlamydomyxa labyrinthuloides shares morphological features with xanthophytes and chrysophytes, whereas pigment composition indicates a grouping with the phaeophytes, raphidophytes and chrysophytes. The sequence of the SSU rRNA gene and its phylogenetic reconstruction unambiguously demonstrate that Chlamydomyxa labyrinthuloides is related to the chrysophytes.