The archaeologists were excavating at the 1350-year-old Balatlar Church in the Black Sea province of Sinop, reports the Hurriyet Daily News.
They unearthed a stone chest, containing the cross fragment, along with the skeletons of more than 1000 people.
"We have found a holy thing in a chest. It is a piece of a cross." said Professor Gülgün Köroğlu, head of the excavations.
"This stone chest is very important to us. It has a history and is the most important artifact we have unearthed so far," she said.
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"During the excavations, we have seen many things that we didn't know about before," Professor Köroğlu said. "Sinop has gained a very good ancient site that we will show visitors."