The effect of the alternation of light/dark periods (AL) (16/8 min light/dark cycles and a photosynthetic photon flux density (PPFD) of 50 μmol photons m(-2) s(-1) for three days) to clarify the mechanisms involved in the clomazone tolerance of tobacco plantlets primed with AL was studied. Clomazone decreased PSII activity, the net photosynthetic rate (Pn), and the ascorbate and total polyphenol contents and increased H2O2 and starch grain accumulation and the number of the cells that underwent programmed cell death (PCD). The pretreatment with AL reduced the inhibitory effect of clomazone on the PSII activity and photosynthesis, as indicated by the decreases in the H2O2 and starch grain accumulation and the PCD levels, and increased the content of ascorbate and certain phenolic compounds, such as chlorogenic acid, neochlorogenic acid and rutin. The AL treatment could promote photorespiration via post-illumination burst (PIB) effects. This alternative photorespiratory electron pathway may reduce H2O2 generation via the consumption of photochemical energy, such as NADH+H(+). At 10 days (D10) of AL treatment, this process induced moderate stress which stimulates H2O2 detoxification systems by increasing the activity of antioxidant enzymes and the biosynthesis of antioxidant components. Therefore, the PCD levels provoked by clomazone were noticeably decreased.