Chrysodidymus represents a monotypic genus of silica-scaled chrysophytes, with well characterised morphology and ultrastructure, as well as pretty known ecology. However, the taxonomic status of this genus remains ambiguous due to the absence of relevant sequence data. In this study, we have aimed to genetically characterize a newly established C. synuroideus culture to elucidate the taxonomy of Chrysodidymus. Our multigene SSU rDNA + LSU rDNA + rbcL phylogenetic analysis inferred C. synuroideus to be significantly nested deeply inside the genus Synura. This convincing evidence led us to propose a new combination for this taxon – Synura synuroidea (Prowse) Pusztai et al., comb. nov.