Hughes reportedly returned to New Mexico on leave in July 1983.
His true identity came to light during a passport fraud investigation being conducted by the Department of State's Diplomatic Security Service, officials stated. On December 1983, the Air Force declared Hughes a deserter. Inside his townhouse they discovered a to-do list and a list of books Hughes planned to read upon his return.
Hughes had been claiming to be an individual named Barry O'Beirne but admitted that he was actually named William Howard Hughes, Jr. and that he had deserted the air force, the OSI said. Others speculated that he had defected -possibly to the Soviets - with the highly classified information, a notion that fomented conspiracy theories for years.
Hughes, now 66, has been charged with desertion.
At the time of his disappearance, Hughes was in his early thirties.
But more than 30 years after he dropped off the grid, Hughes was caught.
Although Hughes told the authorities he abandoned his air force career because he had gotten "depressed", and assumed a fake identity before settling down in California, the AFOSI authorities said there were a number of questions that still remain unanswered regarding his disappearance, which will be revealed as investigation into his actions continued.
His family did not appear to know about his disappearance with the Albuquerque Journal reporting that his sisters said at the time that they thought he might have been abducted.
As Capt Hughes vanished during the Cold War, there was speculation that he had been abducted by the Soviet Union - or defected to them.
Upon launching its investigation into Hughes, the Air Force did not immediately rule out defection as a possibility, according to 1984 newspaper accounts in the Albuquerque Journal in which a public affairs officer said it is one "option". Secret and NATO Secret information, " the Air Force maintained that he was not carrying classified information with him on his trip to the Netherlands.
But an Office of Special Investigations spokesperson Linda Card told the Albuquerque Journal there was no indication Hughes was involved with the Soviet Union or that any classified information was leaked. But still, she said, the case remains under investigation.
"Until we have the whole story, we don't have the story", Card said.
Hughes was taken into custody without incident and is at Travis Air Force Base in California awaiting pre-trial confinement, the Air Force said.
Desertion carries maximum penalties of dishonorable discharge, forfeiture of all pay and confinement of five years.