This study demonstrated promising results for microwave-assisted extraction (MAE) of antioxidative anthraquinones from roots of a medicinally important plant, Morinda citrifolia. The effects of temperature, ethanol compositions, and types of solvents on the percent recovery of the extract were determined. The extraction recovery and the antioxidant activity of the extract were compared with those of the extracts obtained from the conventional methods including ultrasound-assisted extraction (UAE). The percent recovery of anthraquinones was found to increase with increasing MAE time and temperature, and was highly dependent on the type of solvents used. Among the four solvents tested (acetone, ethanol, methanol, and acetonitrile), methanol gave the highest recovery. Furthermore, it was found that the anthraquinones recovery was also affected by the amount of water present in the extraction solvent. This was due to the relative polarity and swelling of plant tissue matrix by water. To achieve the same recovery as with MAE, maceration, soxhlet extraction, and UAE required much longer time. In addition, the antioxidant activity of the MAE extract was found to be only slightly lower than that of soxhlet extraction but significantly higher than those obtained by maceration and UAE.