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Background: Arugula is an essential oil crop of cruciferous species worldwide and serves as a salad vegetable. Purple plant leaves provide nutrients benefiting human beings and are mainly attributed to high anthocyanins. In this study, we collected a purple arugula cultivar with purple leaves and a green arugula with green leaves. The genetic bases and mechanisms underlying purple leaf formation in arugula remain unclear. Therefore, we conducted integrative metabolomics and transcriptomics of two arugula cultivars with different leaf colors. Methods: To study the underlying mechanisms, transcriptomic and metabolomic analyses were carried out. Results: Metabolomic analysis revealed that 84 of 747 metabolites were significantly differentially expressed, comprising 30 depleted and 49 enriched metabolites. Further analysis showed that cyanidin is the main components responsible for the purple color. A total of 144,790 unigenes were obtained by transcriptomic analysis, with 13,204 unigenes differentially expressed, comprising 8120 downregulated and 5084 upregulated unigenes. Seven structural genes, <i>PAL</i>, <i>C4H</i>, <i>4CL</i>, <i>CHS</i>, <i>CCoAOMT</i>, <i>LDOX</i>, and <i>UFGT</i>, were identified as candidate genes associated with anthocyanin accumulation through combined analysis of transcriptome and metabolome. Conclusions: Collectively, the differences in the expression levels of <i>PAL</i>, <i>C4H</i>, <i>4CL</i>, <i>CHS</i>, <i>CCoAOMT</i>, <i>LDOX</i>, and <i>UFGT</i> might be responsible for purple leaf coloration, providing important data for the discovery of candidate genes and molecular bases controlling the purple leaves in arugula.