Understanding the ecology and evolution of the cnidarian-algal symbiosis is of major scientific interest as it is sensitive to temperature and strong light and may therefore be susceptible to climate change. The stability of this mutualism is often mediated by host color pigments that influence photosynthetic activity in symbiotic dinoflagellates either by providing the photosystem with irradiance of suitable wavelength or by protecting it from much too much and potentially damaging light. Like scleractinian corals, the upside-down jellyfish, Cassiopea andromeda, relies heavily on the nutrients provided by its symbionts of the dinoflagellate genus Symbiodinium. It occurs in several conspicuously different color morphs and is found in habitats with high levels of irradiation. We tested whether the color morphs of Cassiopea were correlated with the Symbiodinium distribution in the host and whether host color was associated with different clades of Symbiodinium. We found that the presence of color pigment did not correlate with the distribution of Symbiodinium in the host. Symbiodinium was found in both the colored tentacles of the jellyfish and the colorless feeding tentacles. At least six different color morphs co-occurred in the very shallow waters of the Red Sea, but they all hosted a single Symbiodinium clade (clade A1). Therefore, no correlation of host color morph and Symbiodinium clade could be found. Photoaccumulative or photoprotective functions of host pigments, as proposed for some scleractinian corals, thus seem unlikely in the colored tentacles (vesicles) of the upside-down jellyfish Cassiopea andromeda.