ABSTRACTThe green amoeboid cells of Chlorarachnion reptans Geitler are completely naked and each contains a central nucleus, several bilobed chloroplasts each with a central projecting pyrenoid enveloped by a capping vesicle, several Golgi bodies, mitochondria with tubular cristae, extensive rough ER, and a distinct layer of peripheral vesicles. Complex extrusome‐like organelles occur rarely in both the amoeboid and flagellate stages. The only organelles entering the reticulopodia are mitochondria, but microtubules are also present. The chloroplasts contain chlorophylls a and b, but histochemical tests suggest that the carbohydrate storage product probably is not a starch. The chloroplast lamellae are composed of one to three thylakoids or form deep stacks. A girdle lamella and interlamellar partitions are absent. Each chloroplast is bounded by either four separate membranes, a pair of membranes with vesicular profiles between them, or three membranes; all three arrangements may occur in the same chloroplast. A periplastidal compartment occurs near the base of the pyrenoid where there are always four surrounding membranes. The compartment has a relatively dense matrix and contains ribosome‐like particles and small dense spheres; it extends over and into a deep invagination in the pyrenoid where its contents are enclosed in a double‐membraned envelope which is penetrated by wide pores. The zoospores are ovoid and each bears a single laterally inserted flagellum which appears to be wrapped helically around the cell body during swimming. The flagellum lies in a groove in the cell surface and bears fine lateral hairs. Neither a second flagellum or vestige of one, nor an eyespot, is present. A single microtubular root and a larger homogeneous root run from the flagellar base parallel to the emerging flagellum, between the nuclear envelope and the plasmalemma. In the simple flagellar transition region, fine filaments connect adjacent axonemal doublets. A detailed comparison of C. reptans with all other algal taxa results in the conclusion that it must be segregated in the new class Chlorarachniophyceae, the only class in the new division Chlorarachniophyta. The possibility that C. reptans evolved from a symbiosis between a colorless amoeboid cell and a chlorophyll b‐ containing eukaryote is considered, but the possible affinities of the symbiont remain enigmatic. The implications of the unique chloroplast structure of C. reptans for current hypotheses concerning the origin of chloroplasts are discussed.