Chrysodidymus cell bodies are covered with a single layer of silica scales. They are slipper-shaped with an apical spine. The spine is longer on scales found at or near the anterior end of the cell.

Scales are found on all parts of the cell body except where the posterior ends of the cells adjoin. There are no obvious structures that connect the two cells; presumably, an adhesive of some sort is present that does not interact with electrons (and therefore is invisible to electron microscopy).

Scales also appear on both flagella. The longer, anterior flagellum bears tripartite tubular hairs. These hairs are typical for members of the stramenopile lineage.

The shorter, posteriorly-directed flagellum has a two-part flagellar swelling near its proximal end (the "base" of the flagellum). This flagellar swelling fluoresces green when illuminated with violet or near-ultraviolet light. This autofluorescence is associated with photoreceptor (light-absorbing) domains in golden algae and other protists that are associated with phototaxis (the ability of cells to swim towards or away from light).

The transition region of both flagella has a coiled fiber (transitional helix) of six gyres. Many stramenopiles have transitional helices.

The two flagellar basal bodies are located at the anterior end of the cell. They are nearly parallel to each other. Associated with the basal bodies is a single microtubular root ("root R1") that forms a loop around the anterior end of the cell. From this microtubular root, cytoskeletal microtubules descend towards the posterior end of the cell. There is also a striated fiber (rhizoplast, System II fiber) that extends between the basal bodies and the nucleus. This configuration of structures (the "kinetid" or "flagellar apparatus") is characteristic for members of the "synurophyte" golden algae.

As in other golden algae, the mitochondrial cristae are tubular, and the chloroplasts have three-thylakoid lamellae and are bounded by rough endoplasmic reticulum (the "chloroplast endoplasmic reticulum"). In many golden algae, the chloroplast endoplasmic reticulum is continuous with the nuclear envelope, but this features is not apparent in Chrysodidymus or other "synurophyte" algae. As with other "synurophyte" algae, the scales are formed in the chloroplast endoplasmic reticulum on the side of the chloroplast that faces the cell surface. The large vacuole in the posterior end of the cell is presumed to contain chrysolaminarin, the storage polysaccharide.

There are a number of vacuoles in the anterior end of the cell. Their function is unknown.

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