Since then, Dr. Aydingun’s team and researchers from eight foreign universities have found a second, older port on the peninsula’s eastern side, its Greek influences suggesting that it dated to about the second century B.C.

Nearby, atop the round foundations of a Greek temple, they found the remains of a fifth- or sixth-century Byzantine church and cemetery with 20 burials, and a large stone relief of a Byzantine cross. Coins, pottery and other artifacts indicate that the church suffered damage in the devastating earthquake of 557 but was in use until 1037, when a tremor leveled it — crushing three men whose bodies were found beneath a collapsed wall, along with a coin bearing the image of a minor emperor who ruled during the year of the quake.

After bushwhacking through nettle-choked underbrush a mile and a half north of the harbor, the researchers excavated a 360-by-90-foot open-air cistern or pool, as well as walls and foundations from several multistory buildings that may have been part of a villa or palace altered over many centuries.

Because the archaeologists are at the beginning of a multiyear dig at a site not known from historical sources, they are hesitant to draw many conclusions. Even the name Bathonea is a placeholder, inspired by two ancient references: the first-century historian Pliny the Elder’s “Natural History,” which refers to the river feeding the lake as Bathynias; and a work by a ninth-century Byzantine monk, Theophanes, who called the region Bathyasos.

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“There is a big question mark over the name,” Dr. Aydingun said. “It’s too early to say. But the name is not important. The important thing to note is that there are buildings, roads” where “people thought there was nothing.”

“But there’s something there,” she went on. “We need a lifetime to discover what it is. But even by next year, we’ll be able to say more.”