Few small places have switched allegiances as often as Larymna. It began as a town of the Opuntian Locrians, and the poet Lycophron counted it among the holdings of the hero Ajax the Lesser, son of Oileus. Later it was reckoned part of ancient Phocis, and later still it joined Boeotia. The geographer Pausanias records that it changed sides willingly, attaching itself to the Boeotian League as the power of nearby Thebes grew. The timing is murky, and an old sailing manual still listed it as Locrian after Thebes had already risen, so the shift may have come only after the city was rebuilt by Cassander in the late fourth century BC. By 230 BC the records call it Boeotian, and Boeotian it remained into the era of the Roman general Sulla. Even then, out of long habit and old loyalty, people kept calling it "the Locrian Larymna."

About a mile and a half from the upper town, on the coast, stood its harbor. As Larymna threw in its lot with the Boeotian League, that port grew steadily more useful, becoming the most convenient outlet to the eastern sea for a cluster of inland Boeotian towns, Lebadeia, Chaeroneia, Orchomenus, Copae, and others. Trade flowed to the coast, and the coast prospered. The two settlements came to be told apart by position: the inland Upper Larymna and the coastal Lower Larymna, the latter increasingly the busier and more important of the pair. When the Romans formally united the two, the people of the upper town were most likely resettled at the port, and Upper Larymna was simply abandoned, a hilltown emptied so its harbor could thrive.

Because the lower town outlived the upper, later visitors often knew only one Larymna. Pausanias mentions a single town, and the fact that he says nothing about a river surfacing from underground is itself a clue that he never climbed to the upper site, for he could hardly have failed to remark on so striking a sight. The ruins of the lower town, called Kastri like those at Delphi, sit among bushes on the Bay of Larmes near the mouth of the Cephissus. In the mid-nineteenth century the British topographer William Martin Leake walked the upper walls and found them less than a mile around, built of a soft red stone badly eaten by the sea air, in places still standing near half their height. He noted a tall ancient tomb on the rocks, its inscription and carved ornaments worn smooth by time, and a small salt pool the locals called the Glyfonero and used as a remedy. Quiet clues, left for anyone willing to look.