These studies were conducted on the twoflavonoid compounds of quercetin and kaempferol in addition electrophoretic studies of esterase and peroxidase isoenzymes by SDS-polyacrylamide gel electrophoresisfor five <em>Cleome</em>L. species. Extraction of these flavonoids was carried out using 90% ethanol and 85% methanol. Identification and quantification of quercetin and kaempferol was done using thin Layer chromatography (TLC) and further augmented using high performance liquid chromatography (HPLC) and then isolated,purified and identified using melting point (M.P.) and infrared spectroscopy (IR).eightquercetinand seven kaempferol compounds are isolated and identified with different percentages. Electrophoretic patterns of two isoenzymes ofesterases (Est) and peroxidases (Prx) considered a good taxonomicmarker techniques. A total 45 esterase and peroxidase bands obtained scanning the gels. The highest combined esterase and peroxidase bands (13 bands) are found in <em>C.scaposa</em> DCwhereasthe lowest seven bands are recorded in <em>C. paradoxa</em> B.BR.35 obtained data of two flavonoid compounds and two isoenzymeswere subjected to numerical analysis which separated the studied species into two groups, the first has <em>C.gynandra</em>. and <em>C. viscosa </em>L., the second group included three species of <em>C. scaposa </em>DC<em>, C. brachycarpa </em>. and<em> C. paradoxa</em>.
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