The great navigator's remains were returned to Portugal in 1538 but his tombstone can still be seen on the south side of the church, set in the floor with a brass rail.
The grave no longer houses the navigator's remains, but his tombstone still stands. 
mnli hypothesis: The grave no longer houses the navigator's remains, but his tombstone still stands.  premise: The great navigator's remains were returned to Portugal in 1538 but his tombstone can still be seen on the south side of the church, set in the floor with a brass rail.