Bryopsidales green macroalgae can induce non-photochemical quenching (NPQ) only slowly, presumably due to the lack of the proton gradient-induced component (qE) of NPQ and xanthophyll cycle. Here, two morphologically rather similar siphonous macroalgae, a Bryopsidales alga Bryopsis sp. and a Dasycladales alga Acetabularia acetabulum, latter of which is capable of qE, were given high light treatments with both constant and fluctuating intensity. No differences in the rate of photoinhibition of Photosystem II (PSII), estimated with the chlorophyll a fluorescence parameter FV/FM, in the absence or presence of lincomycin, were observed between constant and fluctuating light, nor between the two algae. Bryopsis sp. showed slower PSII recovery than A. acetabulum, possibly reflecting a regulatory response rather than increased oxidative stress, as the recovery rates increased with increasing amounts of PSII photoinhibition in both algae. In Bryopsis sp., however, high light treatments led to decreased electron transfer rates, estimated by both chlorophyll a fluorescence and net oxygen production, whereas a stimulation was observed in A. acetabulum. Nigericin, which prevents the formation of qE, increased photoinhibition in A. acetabulum but not in Bryopsis sp. Microoxic conditions as well as inhibitors of plastid terminal oxidase and mitochondrial respiration, on the other hand, enhanced photoinhibition only in Bryopsis sp., suggesting that, in the absence of qE, oxygen-dependent pathways (including flavodiiron proteins) are important for photoprotection. Near-infra-red absorption measurements suggest decreased Photosystem I (PSI) donor side limitation in Bryopsis sp., compared to A. acetabulum, and a lower capacity to keep P700 oxidised.