Hydnophytum formicarum Jack. (Rubiaceae) is a medicinal plant whose tubers possesses cardiovascular, anti-inflammatory and antiparasitic effects and have been used for the treatment of hepatitis, rheumatism and diarrhea. Herein we report the isolation of its active constituents and the testing of their antimicrobial activity against 27 strains of microorganisms using an agar dilution method and of their antioxidative activity using the DPPH and SOD assays. The results show that the crude hexane, dichloromethane, ethylacetate and methanol extracts exert such activities. Particularly, the crude ethyl acetate extract exhibits antigrowth activity against many Gram-positive and Gram-negative bacteria with MIC 256 microg/mL. Shewanella putrefaciens ATCC 8671 is completely inhibited at a lower MIC (128 microg/mL). Interestingly, Corynebacterium diphtheriae NCTC10356 is inhibited by all the tested extracts. Significantly, the ethyl acetate extract is also the most potent antioxidant, showing 83.31% radical scavenging activity with IC50 8.40 microg/mL in the DPPH assay. The other extracts display weak to moderate antioxidative activities, ranging from 28.60-56.80% radical scavenging. The SOD assay shows that methanol extract exhibits the highest activity (74.19% inhibition of superoxide radical). The dichloromethane and ethyl acetate extracts display comparable SOD activity. The promising bioactivities of the crude ethyl acetate extract guided the first isolation of bioactive flavonoid and phenolic compounds: isoliquiritigenin (2), protocatechualdehyde(3), butin (4) and butein (5) from this species. Their structures have been fully established by 1D and 2D NMR. In addition, stigmasterol was isolated from the crude hexane and dichloromethane extracts. The antimicrobial and cytotoxic activities of compounds 3-5 were evaluated. The tested compounds were inactive against HuCCA-1 and KB cell lines,showing ED50> 10 microg/mL. Protocatechualdehyde (3) completely inhibits the growth of Plesiomonas shigelloides with MIC <or=60 microg/mL. As a result, we propose that Hydnophytum formicarum Jack. can serve as a new source enriched with potent antioxidative and antimicrobial agents.