Dinoflagellates in the genus Symbiodinium associate with a broad array of metazoan and protistian hosts. Symbiodinium-based symbioses involving bioeroding sponge hosts have received less attention than those involving scleractinian hosts. Certain species of common Cliona harbor high densities of an ecologically restricted group of Symbiodinium, referred to as Clade G. The relationships of these unusual Clade G Symbiodinium with Foraminifera, sponges, and black coral (Antipatharia) are rarely studied. Nonetheless, analyses of genetic evidence indicate that Clade G likely comprises several distinct species. Here we use genetic data in combination with ecological and geographic evidence to formally describe Symbiodinium endoclionum sp. nov. obtained from the Pacific boring sponge Cliona orientalis and S. spongiolum sp. nov. from the congeneric western Atlantic sponge C. varians. These species appear to be part of an adaptive radiation of Clade G lineages specialized to the metazoan phyla Porifera and Cnidaria that began prior to the separation of the Pacific and Atlantic Oceans.