Officers made the find at Kinnoull Hill, which is a well known woodland area with stunning views of the River Tay and across to Fife on the outskirts of Perth.
The discovery was made during a search for a 55-year-old Perth man, who had been reported missing by his family at 8am.
Police sources suggested the two bodies were found some distance apart on the hill and the deaths are not connected.
The next of kin of both people are currently being contacted.
There are no further details about the identies of either of the bodies, but police said a fuller statement will be released tomorrow.
A spokesman said: "Police Scotland are presently making enquiries with regard to 2 bodies which have been found on Kinnoull Hill, Perth earlier today.
"There is no known connection between the bodies and there are no apparent suspicious circumstances.
"Positive lines of enquiry are being conducted with regard to the identity of each body and next of kin are to be informed."
The hill is topped by Kinnoull Tower, which was built in 1829 by Lord Grey of Kinfauns as a romantic folly, in the style of the German castles along the Rhine.
However, it also has a tragic history as a suicide spot.
The most notorious case was in 2002, when Daniela Smith, 31 pushed her two infant children off the hill's summit while they were strapped in their pushchair. Smith then threw herself off the edge
Meanwhile, a missing 14-year-old schoolgirl from Angus has been found safe and well.
Katelynn McPherson had been reported missing from her home address in Birkhill earlier in the day. But the search has been called off.