The church, which is more than 1,300 years old, contains massive marble columns as well as exquisite mosaics, the Israel Antiquities Authority said in a statement.
Archaeologists believe that the church, uncovered in Hirbet Madras in central Israel, is the location marked on the Madaba Map as the tomb of Zechariah, according to Haaertz.
"The researchers believe that in light of an analysis of the Christian sources, including the Madaba Map, the church at Hirbet Madras is a memorial church designed to mark the tomb of the prophet Zechariah," the IAA said.
The agency stressed that this is just a theory and requires more research for confirmation.
"This issue will be examined and studied in the near future," the IAA said.
Zechariah is believed to have lived around 500 B.C., according to the website of the Vatican Museums. The book of Zechariah speaks of the return of the Jews from exile in Babylon as well as the coming of the Messiah.
The archaeologists began excavating the site following a robbery there, Haaertz said. It was the first dig at the site, even though a piece of a doorway had been spotted poking out of the ground there in the 1980s.
To the archaeologists' surprise, they found that the church sits on what looks like a structure from the Roman era, as well as a large complex of caves and tunnels used by Jewish rebels fighting the Romans during the Bar Kokhba revolt of A.D. 132.
Besides the ancient church, archaeologists found coins, stone vessels, lamps and ancient pottery.
"There is no doubt the discovery is extraordinary and of great importance in terms of research, religion and tourism," the IAA said, according to Agence France-Presse.