The flight, piloted by Indian captain Bhavye Suneja, was on a short journey to Pangkal Pinang city on October 29. It crashed minutes after the pilot asked for permission to turn back to the airport. The jet was only about two months old.
The flight's first black box, flight data recorder, was found in November, buried in debris on the floor of the Java Sea.
"The Hydrography and Oceanography Centre of the Indonesian Navy, assisted by the National Transportation Safety Committee, discovered the cockpit voice recorder," Rear Admiral Harjo Susmoro, head of the Centre, was quoted as saying by the Washington Post.
The recorder was found around 8.40 a.m. (local time) by a Navy diver, officials said.
Strong currents in the Java Sea previously complicated the search operation as well as the intensity of the crash, which scattered the plane's wreckage all over the deep waters off the coast near Jakarta.
The small, bright orange device was found 108 feet under the sea, buried under mud.
Findings suggest that Lion Air had put the plane back into service despite it having had problems on earlier flights.
According to reports, the pilots appeared to struggle with an automated system designed to keep the plane from stalling. The anti-stalling system repeatedly forced the plane's nose down, despite efforts by pilots to correct it.
Investigators said the plane was not airworthy and should have been grounded.