ABSTRACT Since the 1960s the demand for ornamental aquarium fish has grown steadily and consequently cyanide fishing is still a popular fishing method despite its prohibition. This poses a severe threat to coral reefs in Southeast Asia. This study aimed to investigate the short-term stress reaction on photosynthetic yield in the tissues of three different hard coral colonies (branching growth forms Pocillopora damicornis and Seriatopora hystrix, and massive Porites lobata) to initially high and then decreasing cyanide exposure, mimicking cyanide fishing by fishermen. Experiments were performed both in situ in the coral reefs of the Marine Protected Area Pulau Pieh, West Sumatra, Indonesia, and in the aquaria facilities of ZMT in Germany. A Diving-PAM fluorometer was used for in vivo stress assessment of the holobiont. While in all species the photosynthetic efficiency was significantly reduced right after cyanide application, the massive species displayed much lower ΔF/Fm’ values. After three days in cyanide-free water all three coral species recovered to initial values of Fv/Fm, except for P. lobata. No bleaching or discolouration was detected by the conclusion of the experiment after 38 days. Especially Indonesian reefs with massive corals may be therefore more severely impacted by cyanide fishing since the retention time of the water in these reefs is longer than in reefs that consist primarily of branching corals. This might have implications for the management of different reef parts of the MPA.