Ministeria vibrans (Filasterea) is a tiny amoeboid species described by Tong in 1997. It has been sporadically found in different habitats, and cultured strains were established. M. vibrans is well characterised by molecular phylogeny but until now was not ultrastructurally investigated in detail. Here, we provide the ultrastructure for this species based on a new strain isolated from oxygen-depleted water of the Baltic Sea. A thin vibrating flagellum could be observed but no vibrating movement of the cell body and no stalk. Our first ultrastructural study of a filasterean taxon revealed radial microvilli supported by bundles of microfilaments. Two centrioles located in the nuclear pit can migrate to the cell periphery and transform into the kinetid: the centriole orthogonal to the kinetosome with a fibrillar root and a basal foot that initiates microtubules. Microvilli in Ministeria suggest their presence in the common ancestor of Filasterea and Choanoflagellata. The kinetid structure of Ministeria is similar to that of the choanocytes of the most deep-branching sponges, differing essentially from the kinetid of choanoflagellates. Thus, kinetid and microvilli of Ministeria illustrate features of the common ancestor of three holozoan groups: Filasterea, Metazoa and Choanoflagellata.