Government forces were combing the port, a journalist accompanying the troops said, almost three weeks after the loyalists launched an offensive against the Shiite insurgents and their allies on Yemen's southwestern coast.
An official statement said government forces recaptured the whole city, but a military commander in the field told AFP that loyalists were still fighting the rebels on the southern outskirts of Mokha.
Forces loyal to President Abedrabbo Mansour Hadi launched a vast offensive on January 7 to retake the Dhubab district overlooking the Bab al-Mandab strait, a key maritime route connecting the Red Sea and the Indian Ocean .
Warplanes and Apache attack helicopters from a Saudi-led Arab coalition have been pounding the rebels in support of pro-Hadi forces, military sources said.
Huthis have controlled Mokha since they overran the capital in September 2014 and advanced on other regions aided by troops loyal to former president Ali Abdullah Saleh.
The coalition mounted a military campaign against the rebels in March 2015 as insurgents closed in on Hadi in his refuge in the southern city of Aden and forced him to seek exile in Riyadh.
Loyalists have since drove rebels out of five southern provinces, including Aden.
The World Health Organization says that more than 7,400 people have been killed since the coalition intervention began.
A UN spokesman has said the civilian death toll alone could top 10,000.