Methoxyflavones are flavonoid widely distributed in plants and has been reported as potent antitumor agents and some of them have shown activity against HIV-1. In this work, two methoxyflavones isolated from Marcetia taxifolia were evaluated in vitro and in silico as HIV-1 inhibitors. Pentamethoxyflavone (5,3’-dihydroxy-3,6,7,8,4’-pentamethoxyflavone) (PMF) and Hexamethoxyflavone (5-Hydroxy-3,6,7,8,3’,4’-hexamethoxyflavone) (HMF) showed activity against HIV-1. The EC50 for HMF was 0.05 μM and 0.04 μM for PMF. The methoxyflavones also inhibited HIV-1 reverse transcriptase (RT), with an IC50 of 4.1 μM for HMF and 0.4 μM for PMF. PMF exhibited an IC50 lower than nevirapine (1.4 μM). These results are in agreement with the in silico prediction for the interaction of these flavonoids with RT. Furthermore, the effect of some methoxyflavones with different patterns of methoxylation was evaluated on RT activity in a virtual screening; found that the inhibitory activity was inversely proportional to the degree of methoxylation.