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The redox state of the plastoquinone (PQ) pool in thylakoids plays an important role in the regulation of chloroplast metabolism. In the light, the PQ pool is mostly reduced, followed by oxidation after light cessation. It has been believed for a long time that dark oxidation depends on oxygen, although the precise mechanisms of the process are still unknown and debated. In this work, we analyzed PQ pool oxidation kinetics in isolated pea (Pisum sativum) thylakoids by tracking the changes in the area above the OJIP fluorescence curve (Afl) over time intervals from 0.1 s to 10 min in the dark following illumination. Afl served as an indirect measure of the redox state of the PQ pool that enabled quantification of the rate of PQ pool oxidation. The results showed a two-phase increase in Afl. The “fast” phase appeared to be linked to electron flow from the PQ pool to downstream acceptors of the photosynthetic electron transport chain. The “slow” phase involved oxidation of PQH2 through oxygen-dependent mechanisms. Adding octyl gallate, an inhibitor of plastid terminal oxidase (PTOX), to isolated thylakoid suspensions decreased the rate of the “slow” phase of PQ pool oxidation in the dark after illumination. The addition of either H2O2 or catalase, an enzyme that decomposes H2O2, revealed that H2O2 accelerates oxidation of the PQ pool. This indicates that under conditions that favor H2O2 accumulation, H2O2 can contribute substantially to PQ pool oxidation in the dark after illumination. The contribution of PTOX and H2O2 to the modulation of the PQ pool redox state in plants in the dark after illumination is discussed.