Many flavonoids and isoflavonoids have anti-diabetic effects in animal models. However, the mechanisms that are involved are generally unclear. Since 11β-hydroxysteroid dehydrogenases (HSD11Bs) play important roles in diabetes, we hypothesize that flavonoids and isoflavonoids may affect diabetes by targeting two isoforms of HSD11B differently. The inhibitory effects of flavonoids (apigenin and quercetin) and isoflavonoids [genistein and (±) equol] on rat and human HSD11B1 and HSD11B2 were analyzed. The potencies of inhibition on human HSD11B1 reductase was in the order of apigenin > quercetin > genistein > (±) equol, with IC50 values of 2.19, 5.36, 11.00, and over 100 μM, respectively. Genistein also inhibited rat HSD11B1 reductase with IC50 value of 24.58 μM, while other three chemicals showed no effects on the enzyme activity with IC50 values over 100 μM. However, apigenin and (±) equol did not inhibit human HSD11B2 at concentrations as high as 100 μM, while genistein and quercetin inhibited human HSD11B2 by 60% and 50% at 100 μM, respectively. The effective flavonoids and isoflavonoids are noncompetitive inhibitors of HSD11B1 when steroid substrates were used. Docking analysis showed that they bound to the steroid-binding site of the human HSD11B1. These data indicate that apigenin is a selective inhibitor of human HSD11B1 of two HSD11B isoforms, which may be useful in managing symptoms of the metabolic syndrome.