Cowpea (Vigna unguiculata L. Walp.) is an important legume, and the antioxidant content in cowpea seeds has been recognized as a health-promoting compound for humans. The objectives of this study were to analyze the population structure of cowpea collections and to identify single nucleotide polymorphism (SNP) markers associated with the seed antioxidant content and seed coat colour. A set of 1047 SNPs were used to analyze a 369 cowpea core collection from 47 countries. Results indicated that: (1) there were three clusters in the 369 entries; and the germplasm collected from India, South Africa, and the US showed broader genetic diversity; (2) Scaffold7139_14363 and Scaffold29110_4657 were strongly associated with antioxidant content, and C35063613_1497, Scaffold81493_886, and Scaffold84620_6785 were strongly associated with seed coat colour across three models; (3) significant correlations were detected between the seed antioxidant content and black seed colour (r = 0.45) and between seed antioxidant content and red seed coat colour (r = 0.50); and (4) Scaffold42008_191 and C35082838_2258 were associated with both seed antioxidant content and seed coat colour. The SNP markers identified could potentially be used in marker-assisted breeding to accelerate genetic improvement of cowpea for higher seed antioxidant content.