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Cosmos caudatus Kunth. or “king’s salad” contains high values of nutritional compounds that act as health promoters. Although widely consumed for its medicinal value, information on phytochemical contents and their biosynthesis in the species is scarce. Among the interesting compounds are the anthocyanins that possess a dual role; an antioxidant and natural colorant. A complete anthocyanin biosynthetic pathway in C. caudatus was elucidated using transcriptomics, metabolomics, and anatomical approaches in this study. The transcriptomic analysis revealed genes encoding enzymes in the anthocyanin biosynthetic pathway and the genes encoding the transcription factors relevant to the latter pathway. A total of 11 anthocyanins of cyanidin, pelargonidin, and delphinidin derivatives that are significantly abundant in the species were identified, correlating with the anthocyanin mainstream gene pathway. The occurrence of anthocyanin was further validated by light microscopy. Anthocyanin pigments in C. caudatus were detected at the epidermal layer of the leaf, stem, and flower, and at the cortex of stem and root. To our knowledge, this is the first work that has delineated the complete anthocyanin biosynthetic pathway in Malaysia’s underutilized plant, C. caudatus Kunth. This study correlated multi-omics data that will help integrate systems biology and synthetic biology, for a detailed understanding of the molecular mechanism and characterization of the anthocyanin biosynthesis using heterologous expression studies.