INTRODUCTIONChoanoflagellates are heterotrophic nanoflagellates: small, colorless protozoa that are present in marine and freshwater environments as well as in hydrated soils. Because they are the closest living relatives of the metazoa, the study of their cell biology and genomes promises to provide new insights into metazoan ancestry and origins. They occur as spherical to ovoid cells exhibiting morphological similarities to the choanocytes (feeding cells) of sponges. Specifically, they are characterized by a single anterior flagellum surrounded by a funnel-shaped collar composed of 30 or more actin-based tentacles or microvilli. These structures can be visualized by staining for actin and β-tubulin. In this protocol, Monosiga brevicollis cells are fixed in dilute formaldehyde, attached to coverslips, and then exposed to antibodies against β-tubulin and an actin-specific stain; a simple DNA stain highlights the nucleus. The central challenge of this protocol is to treat the cells gently so that they retain their ultrastructure and remain attached to the coverslips during processing.