The frequency of mitosis of zooxanthellae in a range of symbiotic cnidarian associations was measured over a 24‐h period. Populations of intracellular zooxanthellae in a variety of sessile benthic hosts showed asynchronous division patterns, but those of Mastigias sp. are extracellular in the mesoglea and show phased division with a mitotic index (MI) peak of 11% at 0445 hours. This pelagic medusa swims horizontally during the day in oligotrophic surface waters and vertically and continuously at night, periodically visiting a nutrient‐rich chemocline at 15 m. This periodic exposure to nutrients may contribute to phasing of cell division.In situ growth rates (µ) and doubling times (T) estimated from diel MI data showed that zooxanthellae whose hosts are exposed to higher ambient nutrient concentrations may have faster growth rates than those of hosts in oligotrophic waters.