Christopher Maffei, 43, was arrested Sept. 7 after a four-day pursuit by authorities, when the stolen yacht ran out of gas off of the Monterey Peninsula, according to the district attorney's office.
His children, a boy and girl ages 2 and 3, were found on board and recovered safely.
Maffei allegedly abducted the children at about 3 p.m. on Sept. 4 from the home of their grandmother, who lives in the 100 block of James Court in South San Francisco.
He then drove in a rental car to Alameda where he sailed away with them, police said. Authorities at the time speculated he might be trying to reach Mexico.
The yacht, "Unleashed," was spotted about 50 miles off of the coast from Pillar Point Harbor in San Mateo County early Friday by the operator of a commercial fishing ship who notified the U.S. Coast Guard.
Coast Guard officials sent crews by air and by sea to find the yacht and eventually found Maffei and the two children on board the vessel.
Court records show that Maffei's wife had obtained a temporary restraining order against him shortly before the alleged kidnapping.
Maffei is scheduled to return to court on Nov. 20 for a preliminary hearing. He remains in custody in lieu of $500,000 bail.