The ultrastructure of the choanoflagellate Codosiga botrytis is described with particular reference to the flagellar appendages, the flagellar rootlet system, the transition zone, the basal body and accessory centrioles, and the stalk. The controversial early reports of flagellar appendages in this species have been confirmed and they have been detected in 2 further species, Salpingoeca frequentissima and Monosiga sp. The appendages consist of a delicate bilateral vane 2 mum wide on either side of the axis, composed of extremely fine overlapping or interwoven fibrils. The flagellar root system consists of a large number of radiating microtubules associated with bands of electron-dense material near the basal body; striated roots are absent. The microtubules extend from several separate foci, those in any one group originating near a composite electron-dense band, and for a distance of 300 nm from the basal body they are separated by blocks of interstitial material. The flagellar basal body forms one of a diplosome pair of centrioles. The triplet microtubules of the accessory centriole are embedded in amorphous electron-dense material and the whole is enveloped in a sheath of similar appearance. The existence of a third centriole close to the diplosome pair is also reported. The relatively complex structure of the flagellar transitional zone is described. The stalk is composed of a core of circular lacunae, which may or may not contain finger-like protoplasmic extensions of the posterior end of the cell, surrounded by a continuation of the sheath material which encloses the remainder of the protoplast. In the stalk only there is a further closely sheathing layer about 15 nm thick which is regularly striated, the spacing of the striations in shadowcast material and sections being about 3 times that measured by negative staining. The structure of choanoflagellates differs widely from that of the algal class Chrysophyceae, the group in which they are included in some classifications, and from the remainder of the algae; they do not appear to have a place in either the algae or the plant kingdom. The structure of Codosiga botrytis is briefly compared with that of sponge choanocytes and collared cells in the Metazoa and some of the possible phylogenetic implications of this are indicated.