Background: The genus Indigofera belongs to the family leguminasae consisting of about 700 species. which are distributed throughout the tropical regions. Previous phytochemical studies on other species of Indigofera led to the isolation of Flavonoids,Dihydrostilbenes,Triterpenoids. Method: The aerial parts of Indigofera secundiflora was collected in July 2008 in Samaru, Zaria, Nigeria and authenticated at the Herbarium section, Department of Biological Sciences, Ahmadu Bello University, Zaria, Nigeria. The air-dried plant (250 g) was extracted with acetone (2.5 l) at room temperature to exhaustion and then 70%methanol at room temperature.The combined acetone extract (5.2 g), a portion was separated for antibacterial activity, while the rest portion (3 g) was chromatographed on silica gel column using a polarity gradient of N-hexane and N-hexane :ethyl acetate mixtures and then ethyl acetate:methanol mixtures and finally pure methanol,Gel filteration over sephadex LH-20 eluting with methanol and preparative TLC afforded compounds Quercetin(I),Quercetin 3-O-methylether (II) and Quecretin 3,31,5-trimethylether(III). Agar well diffusion assay method describe by was employed in the antibacterial studies with the acetone extract at concentration of 5 and 10 mg/ml respectively, while for the isolated flavonoids, concentrations of 100,200 and 300 μg/ml were used for studies. The standard antibiotics were Gentamicin 10 μg/ml and Ciprofloxacin 5 μg/ml respectively. Results: Phytochemical studies of the acetone extract by a combination of Flash column chromatography, gel filteration over sephadex and preparative thin-layer chromatography afforded Quercetin,Quercetin 3-O-methylether and Quercetin 3,3,5-trimethylether, the flavonoids were identified by comaparison of their 1H and 13C-NMR spectra with literature data. Antibacterial studies of the extract and isolated flavonoids revealed that the extract and the isolated flavonoids showed activity, however Quercetin [I] showed the least activity, Quercetin-3-O-methylether (II) showed significant activity against Staphylococcus aureus, while Quercetin 3,3’,4’-trimethylether (III) showed activity against all the tested pathogens. T Conclusion: Chemical investigation of the acetone extract of the aerial parts of I.secundiflora led to the isolation of three flavonoids for the first time from this plant,anti-bacterial studies of the extract and the isolated compounds showed activity against the pathogens used with Quercetin being the least active.