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The content and structural profile of polyphenols can have an important effect in their bioactivity and health benefits. Previous studies have shown that combination of structurally complementary flavonoids from cowpea and sorghum synergistically enhance bioactivity. The goal of this study was to identify the phenolic profile of potential sorghum and cowpea varieties that have the best synergistic activity. Three cowpea varieties (white, red, and black) and 3 sorghum varieties (white, lemon yellow, and red) were analyzed using normal and reverse phase HPLC and reverse phase UPLC-TQD-MS. The results showed different flavonoids as major compounds in sorghum and cowpea varieties. The red cowpea had the highest levels of flavonols (mainly quercetin-3-O-diglucoside) at 471 µg/g sample, followed by a white cowpea with dark brown eye whereas a white cowpea with no eye showed the lowest content at 47.1 µg/g.  The lemon yellow sorghum showed highest content of flavanones (2393 µg/g, mainly eriodictyol-5-O-galactoside, eriodictyol-7-O-galactoside and naringenin-5-O-galactoside) and of flavones (667 µg/g, mainly luteolin-7-O-galactoside). Only the white sorghum variety showed the presence of the flavone, apigenin (5.02 µg/g of sample). Phenolic acid content ranged from 271-624 µg/g in cowpea (mainly protocatechuic aldehyde and trans-feruloylaldaric acid) and 66-2569 µg/g in sorghum (mainly caffeic acid esters). Further, the content of flavan-3-ols in cowpea ranged from 207-2155 µg/g of sample (mainly monomeric catechin-7-O-glucoside). Thus, the results indicate that different cowpea and sorghum varieties provide uniquely different profiles of flavonoids. This provides interesting opportunities for targeted combinations of the pulse and grain in food for enhanced health benefits.