While one-to-one specificity between reef-dwelling hosts and symbiotic dinoflagellates of the genus Symbiodinium may occur, detailed examination of some hosts reveals that they contain multiple symbiont types. Individuals of the foraminifer Amphisorus hemprichii living in Papua New Guinea contained mixed communities of Symbiodinium dominated by symbiont types in clades C and F. Moreover, the types showed a distinct pattern in their distribution across the radius of the foraminifer, with clade F Symbiodinium more prevalent in the center of the host cell. The mixed community of symbionts and their pattern of distribution within the foraminifer is likely the result of processes happening both inside the foraminifer and in its external environment. Persistent mixed symbiont communities in foraminifera may be stabilized through benefits conferred by maintaining multiple symbiont lineages for symbiont shuffling. Alternatively they may be stabilized through a heterogeneous internal host environment, partitioning of symbiont functional roles or limitation of symbiont reproduction by the host. Six factors generally determine the presence of any particular symbiont type within a foraminifer: mode of transmission, availability from the environment, recognition by the host, regulation by the host, competition between lineages, and fitness of the holobiont.