The genus Chrysodidymus was first described in 1962 by G. A. Prowse as part of a survey of freshwater algae on the Malayan peninsula. The genus name is derived from Greek words meaning "golden" and "twin", a reference to the morphology of the two-celled colony.

Prowse described two species, C. synuroideus and C. gracilis, on the basis of apparent size and shape differences in populations of cells from natural samples. Since the range of sizes and morphologies were found in a single clonal culture, Graham and coworkers, in 1993, merged the two species under the name C. synuroideus (which is sometimes misspelled C. synuroides).

Graham et al. also established that the two-celled colony is a consistent feature of C. synuroideus. The scales of this species closely resemble those produced by some species in the genus Synura. The species of Synura form multicellular colonies, and some phycologists had speculated that the two-celled colony was the response of a Synura to a suboptimal environment.

On the basis of scale morphology, C. synuroideus is most closely related to Synura sphagnicola (Korshikov) Korshikov, which is found in similar habitats to C. synuroideus and is considered to be the most acidophilic of the Synura species.

It remains to be seen whether C. synuroideus represents a distinct evolutionary lineage or is a morphologically unusual member of the genus Synura.

For information on the classification of Chrysodidymus, see the Classification page.

For lookalike taxa see Similar genera.

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