The latest attempt to reach an agreement between Zelaya and the de facto government comes days after the ousted president pulled his negotiators out of talks.
The two sides remain at odds over whether Zelaya should be reinstated as president before a presidential election scheduled for November 29.
Zelaya remains holed-up at the Brazilian embassy in Tegucigalpa after re-entering the country in late September, two months after he was forced from the presidential palace and into exile.
As the US representatives met the Honduran rivals, a rally by hundreds of pro-Zelaya protesters in Tegucigalpa was broken up by police who fired tear gas.
Barack Obama, the US president, has faced criticism from human rights groups who say that Washington should do more to pressure Micheletti.
At one point in the crisis, the de facto president ordered restrictions on civil liberties to be imposed, during which time media stations suportive of Zelaya were taken off-air.
Complaint against Brazil
The resumption in negotiations on Thursday came a day after Honduras de facto leadership, which is not recognised internationally, lodged legal proceedings against Brazil at the International Court of Justice in The Hague.
The interim government accuses Brazil of interfering in Honduras' internal affairs by sheltering Zelaya at its emabassy in Tegucigalpa, claims dismissed by the Brazilian government.
"The de facto Honduran government has no legitimacy to lodge a law suit in the International Court of Justice," a spokesman for Brazil's foreign ministry said.
Zelaya was forced from power on June 28, the same day that he planned to hold a non-binding referendum on the constitution that had been declared illegal by the Honduran congress and supreme court.
Opponents of Zelaya say that the public vote was aimed at winning support for an extension to presidential term limits, claims that the deposed leader has denied.