On Saturday and Sunday, USC archaeologists and students dug up his remains before new construction began at the legendary racetrack.
The thoroughbred race course and poker card room in Inglewood is being torn down and replaced by a residential and retail complex.
"He was the people's horse and that's why he got his own special burial at Hollywood Park," said USC professor Tom Garrison. "There's a reason why this horse was chosen to be exhumed and reburied. He has that level of meaning in Southern California."
Native Diver was the first California bred horse to win more than a million dollars, which was an incredible amount in the 1960s. He won 34 stakes races and three consecutive Hollywood Gold Cup races, before dying of colic in 1967 at the age of eight.
For most archaeologists, this is not a typical dig.
"We are accustomed, in the area of the world that I work, to dealing with objects that are 2,000-1,500 years old, and of course this is 47 years old. We thought of it as a great teaching opportunity for our students," said Garrison.
It said Native Diver knew he was a star, and even in death, he seemed ready to race.
"The first thing we thought was 'wow, that's a big horse,' but it turned out that he landed on his right side and sort of fell into a position where his legs were extending out. It looked like he was still running his last race," said Garrison.
When Native Diver's bones were dug up, they were almost in perfect condition. If they would have been left where they were found, they would have been destroyed when new construction began at Hollywood Park.
The remains of the thoroughbred are being moved from the old Hollywood Park racetrack to Del Mar racetrack in San Diego.
The Associated Press contributed to this report.