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C-boivinopyranosyl flavones have rarely been isolated from nature. In the search for anti-HBV (hepatitis b virus) constituents of Alternanthera philoxeroides, two new compounds, luteolin-6-C-β-d-boivinopyranosyl-3′-O-β-d-glucopyranoside (1) and chrysoeriol-6-C-β-d-boivinopyranosyl-4′-O-β-d-glucopyranoside (2), along with three known C-boivinopyranosyl flavones (compounds 3–5) were isolated. Their structures were determined by spectroscopic analyses including 1D and 2D NMR, HR-ESI-MS, IR spectra. Compounds 1, 2 and 3 showed significant anti-HBV activities through specifically inhibiting the secretion of HBsAg in HepG2.2.15.