Background Flavonoids are considered as key compounds in honey for their contribution to honey color, taste, flavor and also beneficial health effects. Flavonoids may also be used as biomarkers to fingerprint floral origin of honey since two decades ago, and hence various methods have been developed for the determination of flavonoids and botanical classification of honey using chromatographycal methods such as high-performance liquid chromatography (HPLC). These compounds have been determined in some pollen of flowering plant. Materials and methods In this study determination of pollen flavonoids in three species of bee forage legumes consist of Coronilla varia L. Melolotus officinalis L. and Lotus corniculatus L. from Markazi Province, Iran were conducted by 2-dimensional paper and thin layer chromatography, UV spectroscopy and available references. Results Results showed that some flavonoids such as Kaempferol and Rutin were found in all of studied taxa pollen grains. Luteolin and Quercetin were found in M. officinalis and L. corniculatus while c. varia lacked these flavonoids. The current finding will provide useful information for medicine quality and classify unifloral honey. Conclusion The current finding will provide useful information for evaluation of food and medicine quality of Iranian natural honeys. It helps us to classify the Iranian natural honeys and choosing the specific honey for our specific health-promoting effects.