Chlorine (Cl₂) is a commonly used biocide; however, the cellular mechanism and pathways associated with Cl₂ exposure in algae have not been elucidated. Here, we investigated the physiological and gene transcriptional responses in the dinoflagellate Prorocentrum minimum upon chlorination, with emphasis on the photosynthetic system. The time-course stress response of P. minimum was assessed by measuring transcription of photosynthesis-related genes, chlorophyll autofluorescence (CAF), and photosynthesis efficiency (F _v /F _m ), in response to a series of Cl₂ doses (0.1, 0.5, and 1.0 mg L⁻¹). CAF data showed a marked reduction in fluorescence intensity with increasing Cl₂ doses and exposure time (0, 6, 12, and 24 h). F _v /F _m dramatically decreased after 1 mg L⁻¹ Cl₂ exposure. Transcriptional responses of the photosystem related genes (PmpsbA, PmatpB, PmrbcL, and PmpsaA) were analysed using quantitative real-time (qRT)-PCR. PmpsbA transcription was significantly upregulated in 0.5 and 1.0 mg L⁻¹ of Cl₂ after a 24 h exposure. However, the transcriptional expressions of PmatpB and PmpsaA were downregulated. Our results suggest that photosynthesis-related genes such as PmpsbA may act as indicators of environmental stress response and can be useful and rapid biomarker candidates for ecotoxicogenomic assessments.