The boats, both from south China's Guangdong province, were lost Sunday afternoon as they attempted to navigate gales near the Xisha islands, 330 km from China's island province of Hainan, reported Xinhua citing the Hainan maritime search and rescue centre.
By Monday, rescuers had retrieved 13 survivors, sources said, adding search and rescue operations are continuing.
A total of five fishing boats with 171 people aboard were caught in Typhoon Wutip, the 21st of the season.
China's maritime authority Sunday upgraded its wave warning from yellow to orange, the second-highest of a four-tier colour-coded weather warning system, as the typhoon approached land.
The National Marine Environmental Forecasting Centre warned of storm tides from Sunday to Monday in Guangdong, Hainan and Guangxi.