It plummeted into the Java Sea – no survivors have been found, nor has the body of the Boeing 737.
There is as yet no indication of what caused the crash, though there are reports the aircraft had experienced technical problems on earlier flights.
The plane was making a one-hour journey to the western city of Pangkal Pinang when it went down.
The pilot had asked air traffic control for permission to turn back to the airport, but then contact was lost.
Buried on the sea floor
A diver told reporters on board one of the search and rescue vessels scouring the Java Sea: “We dug and we got the black box.”
The diver, identified as Hendra, said the box had been buried in debris on the sea floor, Reuters reports.
Local news channel Metro TV showed footage of the box, inside a plastic crate, being brought onto a ship.
Recovering the flight recorder means aviation safety experts can begin piecing together the plane’s final moments to work out what went wrong.
Lion Air, a budget airline based in Indonesia, has sacked its technical director, Muhammad Asif.
Representatives from Boeing are meeting Indonesian officials on Wednesday as part of the investigation.