In recent years, the diversity of symbiotic dinoflagellates of the genus Symbiodinium has become intensively investigated. Found in a variety of marine invertebrate hosts, Symbiodinium are a key element in the observed high diversity within many sub-tropical and tropical shallow marine ecosystems. One group of marine invertebrates for which Symbiodinium diversity has been examined is zooxanthellate zoanthids (Cnidaria: Anthozoa: Zoantharia) of three genera; Zoanthus, Isaurus and Palythoa. Focusing on specimens in southern Japan, zoanthid species from Zoanthus and Palythoa show varying patterns of both levels of Symbiodinium variation within individual colonies, and levels of Symbiodinium variation (=“flexibility”) over geographic ranges (i.e., latitudinal/longitudinal variation, etc.). Here I examine and compare the results of previous studies based primarily on sequences of internal transcribed spacer of ribosomal DNA (ITS-rDNA), and focus on two zoanthid species with apparently very different Symbiodinium symbiotic system characters; Zoanthus sansibaricus and Palythoa tuberculosa. Symbiodinium (subclade C1z) within Z. sansibaricus are characterized by extremely high levels of ITS-rDNA sequence microvariation, while Symbiodinium within P. tuberculosa (subclade C1/C3) do not have such microvariation. I suggest that three factors may potentially contribute to apparently higher flexibility and diversity of Symbiodinium in Z. sansibaricus; 1) multiple copies of ITS-rDNA sequences, 2) strong reliance on sexual reproduction in Z. sansibaricus vs. asexual reproduction in P. tuberculosa, and 3) niche specialization by Z. sansibaricus vs. “generalist” P. tuberculosa,. Through an examination of past literature and results, it appears that both multiple intragenomic copies of ITS-rDNA and multiple types of Symbiodinium within Z. sansibaricus due to niche specialization are the most likely reasons behind such unusually high microvariation. It is hoped that in the near future more intensive investigations of Symbiodinium in a variety of host species will help researchers more fully understand the mechanisms driving varying symbiont flexibility and diversity.