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Symbiodiniaceae diversity in hosts is known to change with the environment and particularly with temperature and light intensity. However, higher levels of pCO(2), as could be expected under future ocean acidification scenarios, have been documented to show little to no effect in influencing the diversity of Symbiodiniaceae in hosts in previous studies. In this study, we examined hypervariable psbA(ncr) sequences to identify the Cladocopium (former Symbiodinium 'Clade C') diversity within the zooxanthellate zoantharian Palythoa tuberculosa at an acidified reef in southern Japan. Palythoa tuberculosa were collected from a reef at the volcanic island of Iwotorishima in southern Japan; specimens from a high pCO(2) site and from a nearby control (normal pCO(2)) site (Inoue et al. in Nat Clim Change 3:683-687, 2013). We observed a statistically significant reduction in Cladocopium diversity at the high pCO(2) site with only one Cladocopium lineage present, compared to at the control site with two lineages present. Our results demonstrate that higher pCO(2) can potentially negatively influence the diversity of host Symbiodiniaceae within anthozoan hosts, an important implication in the face of ongoing ocean acidification and climate change.