ABSTRACT Coral reefs, and their associated diverse ecosystems, are of enormous ecological importance. In recent years, coral health has been severely impacted by environmental stressors brought on by human activity and climate change, threatening the extinction of several major reef ecosystems. Reef damage is often mediated by a process called ‘coral bleaching’ where corals, sea anemones, and other cnidarians lose symbiotic photosynthetic dinoflagellate algae (genus Symbiodinium) upon stress induction, resulting in drastically decreased energy harvest and, ultimately, coral death. The molecular mechanisms of this ecologically critical cnidarian-algal symbiosis remains poorly understood. Here, we report a simple microfluidic device with multiple cell traps designed to isolate and image individual live larvae of Aiptasia, a sea anemone model organism, and their algal symbionts over extended time courses. Aiptasia larvae are large (~100 µm in diameter), deformable and motile, posing particular challenges for long-term imaging. Using a trap design optimized with computation flow modeling and empiric testing, we trapped Aiptasia larvae containing symbiotic algae and demonstrated stable imaging for >10 hours. We show algal migration within Aiptasia larvae and observe algal expulsion under an environmental stressor. Finally, we optimized the device for extreme ease-of-use by laboratories unfamiliar with microfluidics. To our knowledge, this device represents the first capable of live imaging of coral larvae and their symbionts and, in further implementation, could provide important insights into the mechanisms of coral bleaching under different environmental stressors.