Butterfly pea (Clitoria ternatea L.) is a climbing legume grown as a medicinal, ornamental, and forage plant, and used as a natural food colorant. Due to its various medicinal properties in different plant parts, pharmacological potential is evident. However, improvement of the plant for high phytochemical properties has been very limited, hence being pursued. For that improvement effort, butterfly pea germplasm was collected from different parts of Thailand in addition to accessions from 12 other countries acquired from a C. ternatea collection curated by the USDA-Agricultural Research Service National Plant Germplasm System. Characterization and evaluation for phytochemical properties of these germplasm is fundamental for breeding purposes. Floral antioxidant activities (Ferric reducing antioxidant power—FRAP and 2,2-diphenyl-1-picrylhydrazyl—DPPH), total phenolic compound (TPC), total anthocyanin content (TAC), and ascorbic acid content (AAC) were investigated for 126 individuals from 46 accessions of the combined collection. The plants were regenerated from seeds and grown at Kamphaeng Saen, Nakhon Pathom, Thailand, and flowers were harvested in August 2017. Significant differences of TAC and AAC were found among the included accessions. Both variations were correlated with petal color at a moderate level, but not in accordance with geographical locations of the samples. Grouping of the accessions based on antioxidant activities and compounds revealed by cluster and principal component analyses would be useful in the utilization and management of the germplasm for butterfly pea improvement.