Friends and supporters accompanied Salvador Mejia-Perez and his wife Elida to San Francisco International Airport Wednesday night.
The couple boarded a flight to Guatemala with their American born four-year-old daughter.
They are leaving their teenage son and daughter behind in Marin County. Immigration officials raided the couple's home by mistake in 2007, found they had no documents and began the deportation process.
An immigration judge had previously ruled the family could stay, but that decision was appealed by the Homeland Security and reversed.
"We worked hard and pay taxes are hoping to stay, but now that is not possible. My family is divided now," said deported mother Elida Perez.
"Our government should not be doing this. They are hard workers and deserve to be here. They were living the American dream, now they're living the American nightmare," said the family's attorney Marc Van Der Hout.
Unless there is a change in their legal status, the deported couple cannot return to the United States for at least the next ten years.