Symbiodinium spp. are well-known symbionts of corals. A number of key species of bioeroding sponges also contain intracellular dinoflagellate symbionts, but little is known about this relationship. The origin and identity of sponge symbiotic inoflagellates is unresolved since theirdiscovery in 1964. Symbiotic bioeroding sponges can invade and kill live corals. If the sponges acquire symbionts during this process, they may act as refuges for vulnerable coral symbionts, as bioeroding sponges appear to be more resistant to thermal bleaching than most corals. To test this hypothesis, pairwise tissue samples from the common brown bioeroding sponge Cliona orientalis Thiele, 1900 and from abutting corals were taken. Samples were obtained from 3 disparate regions of northeastern Australia, extending over more than 1300 km. The genetic identities and population diversities of Symbiodinium from sponges and respective host corals were surveyed using 28S RNA gene sequences. Results suggest that C. orientalis consistently harbours the same clade of symbionts, even in very different environmental conditions. However, populations of sponge Symbiodinium did not appear to be genetically connected between the sampled regions, implying maternal transmission of the symbionts. Furthermore, the sponge zooxanthellae were different to those found in corals. We thus rejected the hypotheses that (1) the sponge acquires its symbionts from invaded corals under normal conditions and (2) that it may offer a refuge to coral symbionts. Symbionts from C. orientalis were closely related to, but distinct from symbionts of soritid foraminiferans, and are likely to belong to a new subclade of G-type dinoflagellates.