Light is an important environmental factor for the growth of Prorocentrum donghaiense Lu, and light intensity is closely related to its growth status. Low light conditions have been shown to be an important factor in the occurrence and continuation of P. donghaiense blooms. However, little is known about the molecular mechanism of the light response of Prorocentrum donghaiense Lu. In the present study, we investigated? for the first time the growth response of P. donghaiense to low light by growth assay, chlorophyll fluorescence assay, transcriptome sequencing analysis and histone lysine methylation modification assay. The growth and chlorophyll fluorescence assays revealed that low light was more conducive to the explosive growth of P. donghaiense, and photosynthetic efficiency was higher. Transcriptome analysis revealed that genes encoding microtubules, microtubule-based processes and structural components of the cytoskeleton were significantly up-regulated under low light, and genes encoding DNA damage and cell cycle arrest were significantly down-regulated. These results were consistent with growth assays of P. donghaiense under different light intensities. Second, transcriptome analysis also revealed genes encoding histone-lysineN-methyltransferase were significantly regulated by light intensity. Western blot experiments revealed many methylation modifications at lysine sites of histone H3 from P. donghaiense and several methylation modifications in response to changes in light intensities. It was hypothesised that histone lysine methylation modification was involved and played an important regulatory role in the growth response of P. donghaiense to light intensity.