The gastrodermal tissues of anthozoans that harbor endosymbiotic Symbiodinium experience light-dependent fluxes in dinoflagellate derived photosynthetic compounds that have the potential to impact the osmotic homeostasis of the animal. To explore this unusual osmoregulatory scenario, genes encoding proteins that play highly conserved roles in osmoregulation (mitogen-activated protein kinases, [MAPKs]) and the maintenance of the cytoskeleton (ß-actin, tropomyosin, and α-tubulin) were quantified over diel cycles using quantitative real-time polymerase chain reaction. The expression of MAPK genes in Pocillopora damicornis increased at night, while the expression of cytoskeleton genes in Seriatopora hystrix decreased. The increase in P. damicornis MAPK expression may reflect host osmolyte production in response to reduced osmotic pressure at night. The concomitant decrease in expression of genes encoding cytoskeleton proteins at night is consistent with this interpretation, indicating reduced production of spatially demanding proteins under periods of intracellular crowding. However, the latter interpretation is confounded by the fact that molecularly-inferred Symbiodinium densities were found to be significantly greater at night in both corals, so changes in cytoskeletal gene expression may also reflect crowding to accommodate the greater density of these endosymbionts. In addition to providing insight into an unusual physiological attribute of photosynthetic endosymbioses, this study represents the first to measure gene behavior in field and cultured corals with a method that considers the dual-compartment nature of the associations.