The U.S. Marine (Public Health Service) Hospital Cemetery is just north of the Main Hospital Building and was coverd with 10 feet of landfill in the 1930's. The WPA added tennis courts and a parking lot around 1933. There is at least one scholar who believes "most" of the bodies were removed, along with their wooden markers, before or around this time but there is no further references to this anywhere.

I don't think the graves were removed completely, if even at all. The Army and Federal Goverment had to do an Environmental Report on the site before it transferred the land to the National Park Service and they found some bodies still below the landfill. The subsequent archaeological report suggests that there are 200 to 999 bodies still buried beneath the padded landscape. ###
FLASH!... the Feds respond.

This next map shows the Presidio Trust Management Plan's suggestions as to how the site should be treated going forward. They rightly believe the cemetery should not be further disturbed. The tennis courts and parking lot should be removed and the whole area planted with native vegetation. A monument or plaque perhaps, should be constructed with all the known names still available so this slight can be somewhat rectified and the matter finally put to rest.

FLASH!... - NEWS UPDATE - October 30, 2011..............
I must report the Presidio Trust has made good on their promise, so far. A recent San Francisco Chronicle article has shown the tennis courts and parking lot are now gone. They are replaced with wonderfully landscaped mounds and vistas. A bench and respectful trail pathways and a brilliant submerged stone monument are clear signs of progress here. (Chronicle Article by Peter Firmrite ( 071911...your assignment - find it yourself - !).