Reverse phase chromatography using C18 stationary phase (i.e. column) can be useful to separate flavonoid compounds. C18 meaning, silica modified with hydrocarbon containing 18 carbon atoms. For extremely hydrophobic compounds, C12 may be useful. Methanol and water can be used as mobile phase (solvents). Alternatively, acetonitrile and water can also be tried. The eluents can be detected by measuring ultra-violet (UV) absorption at wavelength(s) of 290 nm and/or 340 nm. Mass spectrometric detection can also be useful, i.e., LC-MS, where reverse phase LC is combined with mass spectrometry. LC may be done in gradient elution mode, which may result in better separation.

Depending on the polarity of your compound, there are several different methods. Polar ones can be purified by C18, while those that are less polar can be purified on silica.

Here's a summary for various compounds:

http://www.isco.com/WebProductFiles/Applications/101/Application_Notes/AN85_Purification_Strategies_for_Flavones_and_Related_Compounds.pdf

Here's an example from crude extract:

http://www.isco.com/WebProductFiles/Applications/101/Poster_and_Paper_Reprints/Purification_of_Phenolic_Flavonoids.pdf

You can use resin viz. Diaion HP-20, amberlite-XADs for preliminary purification followed by silica (60-120mesh). Finally you can go for C-18 sepak columns or C-18 packing material for individual flavonoids. For purification you can also proceed with flash chromatography, prepHPLC and prep TLC.

Gudluck :)

Thanks for your suggestion.