TELL MARDIKH, Syria — Ali Shibleh crawled through a two-foot-high tunnel until reaching a slightly larger subterranean space. He swung his flashlight’s beam into the dark.

A fighter opposed to President Bashar al-Assad, Mr. Shibleh was roaming beneath Ebla, an ancient ruin that for several decades has been one of Syria’s most carefully studied and publicly celebrated archaeological sites. He had just made another of his many finds: he lifted something resembling a dried stick, then squeezed it between his fingers and thumb.

It broke with a powdery snap. “This is human bone,” he said.

Across much of Syria, the country’s archaeological heritage is imperiled by war, facing threats ranging from outright destruction by bombs and bullets to opportunistic digging by treasure hunters who take advantage of the power vacuum to prowl the country with spades and shovels. Fighting has raged around the Roman ruins of Palmyra, the ancient city in central Syria, once known as the Bride of the Desert. And the Syrian Army has established active garrisons at some of the country’s most treasured and antiquated citadels, including castles at Aleppo, Hama and Homs.

For decades Ebla has been celebrated for the insights it offers into early Syrian civilization. The scenes here today offer something else: a prime example of a peculiar phenomenon of Syria’s civil war — scores, if not hundreds, of archaeological sites, often built and inhabited millenniums ago because of their military value, now at risk as they are put to military use once more.