Antimicrobial activities of flavonoids isolated from the leaves and heartwoods of Artocarpus anisophyllus Miq. and Artocarpus lowii King were evaluated. Gram positive bacteria (Staphylococcus aureus and Bacillus cereus), Gram negative bacteria (Escherichia coli and Pseudomonas putida) and fungi (Candida albicans and Candida glabrata) were used in this study. Disc diffusion method was used as the qualitative assay while minimum inhibitory concentration and minimum microbicidal concentration methods were used as the quantitative assays. Artocarpin (8) showed strong antimicrobial activity towards all bacteria with inhibition zone diameter more than 11 mm and minimum microbicidal concentration value of 0.45 mg/mL. Isobavachalcone (3) exhibited strong antibacterial activity towards Gram positive bacteria with minimum microbicidal concentration value of 0.45 mg/mL. The findings of this study revealed that the isolated flavonoids from A. anisophyllus and A. lowii have potential to be developed as antimicrobial agents.