The plaques, dating from the 1920s, were taken from Woodhenge, which is two miles (3 km) from its more famous contemporary, Stonehenge.
They describe and show a plan of the site, which was discovered by accident in 1925 by a passing RAF pilot.
The plaques were originally installed by the Ministry of Works following archaeological excavations.
Heather Sebire, from English Heritage, which cares for this site, said: "Woodhenge is an incredibly important heritage site and these plaques are a landmark in the history of how the site was discovered, excavated and presented nearly a century ago.
"This is a serious case of heritage crime. We are working with Wiltshire Police and Historic England to identify the culprits and hope we can return the plaques to where they belong."
Phil McMahon, inspector of ancient monuments for Historic England, said: "The sad theft of these historic plaques has deprived us of an important aspect of the story of Woodhenge.
"They represent a key part of one of the earliest attempts to interpret and present to the public the complex and internationally-significant prehistoric monuments of the Stonehenge World Heritage Site.
"We very much hope that the plaques can be recovered and restored to their rightful place at Woodhenge."
Woodhenge dates back to about 2300 BC, and is thought to have been an important communal meeting place for people in the later Stone Age.
Today, 168 concrete posts mark the positions of the original six concentric rings of gigantic timbers, which lay inside a circular ditch called a henge.
Police have appealed for witnesses to contact them.

The man grabbed hold of a child's bag outside Heronsgate School in Lichfield Down, Walnut Tree, at about 08:20 GMT on Wednesday.
The man said, "you're coming with me" before the pupil broke free.
"The incident has been reported to police who are now investigating," the school said. The offender is said to be white and in his 30s.
He had blonde hair and a scratch on his left cheek. He was wearing blue jeans, a blue-green t-shirt and Converse trainers.

The Radio 2 jockey and former Newsnight anchor will be joined by Radio 1 Newsbeat presenter Tina Daheley when the programme returns in September.
They will replace Kirsty Young, Matthew Amroliwala and Martin Bayfield, who have all left the show.
The programme will be shown in a new regular weekly slot, with each episode broadcast live from a "mobile incident studio" near the scene of a crime.
The changes are billed as a revamp for the show, which has been appealing for viewers' information about unsolved crimes since the first episode aired in 1984.
The first four-week series will begin in early September, followed by another block of episodes in early 2017.
Sophie Raworth and Jason Mohammad co-presented episodes earlier this year, but they will now make way for Vine and Daheley.
Crimewatch executive editor Joe Mather said Vine had "the perfect mix of serious journalism alongside genuine empathy towards the victims of crime and their families".
Viewers also know Vine from shows including Points of View, The Politics Show, Panorama and Eggheads, plus as the king of the swingometer in the BBC's election coverage and from his stint on Strictly Come Dancing.
He said: "I grew up watching Crimewatch. It is one of the most powerful programmes the BBC has ever broadcast, with the power to change and save lives, and of course to solve crimes."
Daheley added: "I feel very privileged to join a programme that's allowed ordinary viewers to help bring criminals to justice and make our communities safer.
"Young people often suffer most from crime, so I'm especially keen to use my journalistic skills and experience engaging young audiences at Radio 1 to make sure they feel part of the new-look show."
Follow us on Twitter @BBCNewsEnts, on Instagram, or email entertainment.news@bbc.co.uk.
A pair of bronze plaques have been stolen from a prehistoric monument in Wiltshire.
[NEXT_CONCEPT]
A man tried to abduct a boy outside a primary school in Milton Keynes, the school said.
[NEXT_CONCEPT]
Broadcaster Jeremy Vine is to be one of the new hosts of BBC One's Crimewatch.