show Abstracthide AbstractIn this paper, we conducted a detailed assessment of the physiological toxicity of Polyethylene Terephthalate microplastics (PET-MPs) on the growth of pepper seedlings. Results showed that PET-MPs significantly inhibits the growth of pepper, especially the root growth. Moreover, PET exposure resulted in the burst of ROS, causing oxidative damage. KEGG pathways analysis illustrated that PET-MPs significantly altered flavonoid biosynthesis and phenylpropanoid biosynthesis pathways in both metabolome and transcriptome. Weighted gene correlation network analysis (WGCNA) identified ten structural genes and nine transcription factor genes that play pivotal roles in regulating flavonoid biosynthesis.