Non-photochemical quenching (NPQ) of chlorophyll fluorescence is thought to be an indicator of an essential regulation and photoprotection mechanism against high-light stress in photosynthetic organisms. In this report, special chemicals were used to perturb the kinetics of the Delta pH build-up and the xanthophyll cycle (XC) in Nannochloropsis sp. We found that NPQ was stimulated rapidly on exposure to high light and relaxed rapidly in darkness. The Delta pH could be obligatory for NPQ and DpH alone was not sufficient to induce NPQ. The XC, being strictly mediated by Delta pH, was also essential for NPQ. The results demonstrate that the mechanism of NPQ in Nannochloropsis sp. resembled that of diatoms.