Coreopsis species have been developed to produce cultivars of various floral colors and sizes and are also used in traditional medicine. To identify and evaluate mutant cultivars of C. rosea and C. verticillata, their phytochemical profiles were systematically characterized using ultra-performance liquid chromatography time-of-flight mass spectrometry, and their anti-diabetic effects were evaluated using the dipeptidyl peptidase (DPP)-IV inhibitor screening assay. Forty compounds were tentatively identified. This study is the first to provide comprehensive chemical information on the anti-diabetic effect of C. rosea and C. verticillata. All 32 methanol extracts of Coreopsis cultivars inhibited DPP-IV activity in a concentration-dependent manner (IC50 values: 34.01–158.83 μg/mL). Thirteen compounds presented as potential markers for distinction among the 32 Coreopsis cultivars via principal component analysis and orthogonal partial least squares discriminant analysis. Therefore, these bio-chemometric models can be useful in distinguishing cultivars as potential dietary supplements for functional plants.