Coral reefs are threatened by climate change, because it causes increasingly frequent and severe summer heatwaves, resulting in mass coral bleaching and mortality. Coral bleaching is believed to be driven by an excess production of reactive oxygen (ROS) and nitrogen species (RNS), yet their relative roles during thermal stress remain understudied. Here, we measured ROS and RNS net production, as well as activities of key enzymes involved in ROS scavenging (superoxide dismutase and catalase) and RNS synthesis (nitric oxide synthase) and linked these metrics to physiological measurements of cnidarian holobiont health during thermal stress. We did this for both an established cnidarian model, the sea anemoneExaiptasia diaphana, and an emerging scleractinian model, the coralGalaxea fascicularis, both from the Great Barrier Reef (GBR). Increased ROS production was observed during thermal stress in both species, but it was more apparent inG. fascicularis, which also showed higher levels of physiological stress. RNS did not change in thermally stressedG. fascicularisand decreased inE. diaphana. Our findings in combination with variable ROS levels in previous studies on GBR-sourcedE. diaphanasuggestG. fascicularisis a more suitable model to study the cellular mechanisms of coral bleaching.