I walked down a Phoenician street the other day, built under Persian rule.

A bit bumpy and uneven underfoot – like many a street in modern day Iranian and Lebanese cities – but this one happened to be about 2,600 years old. It ran down to a small harbour, lined by covered stone sewers and drainage ditches on each side, massive door lintels before private homes and a row of shops and warehouses and possibly a temple, five streets and 18 buildings over an area of 3000sq m.

I should say at once that this street constructed under Persian occupation is scarcely two miles from my home on the Beirut seafront, one of the great excavations which the rebuilding of the post-civil war city opened up for future generations, layer after layer of Paleolithic, Phoenician, Greek, Roman and Ottoman Beirut. The place was originally known as "byrt" – which possibly means cistern or well, according to researcher Josette Elayi – then it became Berytos in Greek, Berytus in Latin and now, of course, Beirut. The names are sandwiched together like the layers of streets. This street even yielded up terracotta figures of a woman with outstretched arms, probably the deity Ashtart.

And, true to so much of Lebanese history, Beirut was, in effect, under occupation. In the first millennium BC (875-332BC), all the cities of Phoenicia were under first Assyrian and then Babylonian and then Persian control. Beirut belonged to Sidon – it always seems to belong to someone else – which is now a scruffy Crusader seaside port 30 miles to the south of the modern Lebanese capital. So the coins found in Beirut are Sidonian; the local military power was Sidonian; it was Sidon which dealt directly with the Persians. Beirut was a fishing and trading port, its wooden vessels with their high prows sliding out to Greece, Italy and distant Carthage.

Archaeologists have found sycamore wood here, Egyptian blue pigment, marble, silver, iron, jars for carrying Phoenician olives, olive oil, wheat, walnuts, grapes and wine across the Mediterranean. There's even a stone with a carved graffito of a Phoenician merchant ship, mast fixed with ropes to the sides, two oars tied together as a rudder. It reminds me of the fishing boats carved into the Tudor wood of the old port of Rye, still visible today on the south side of the Sussex churchyard long after the sea has withdrawn from this cinque port.

Today, the Persian-ruled city in Lebanon is exposed beneath the new souks of Beirut. It is part of the city's "Heritage Trail" – in Lebanon, the word heritage means what it says and does not carry the grotty reputation of Britain's tawdry historical re-creations – so that future generations can walk around the old/new city and "watch" its creation over the centuries in Roman streets and Crusader walls, a project overseen by Amira Solh, the young Cornell-trained urban planner who works for Solidere, the company that rebuilt Beirut. She has dreams of an interactive film display behind the underground Persian streets – and promises me there will be no English-style guides flouncing around in Persian costumes. This is serious history for serious people.

Nothing, of course, could be more serious than finding yourself under Persian rule. Roula el-Zein, an archaeologist and consultant for Solidere, described Beirut at the time as "just a small city belonging to Sidon, the city which had all the power". The Phoenicians, she says, "accepted Persian rule after the Babylonians left, and without any problem in assisting the Persian wars against Egypt. Sidon and Tyre were with the Persian kings" – King Baalshillem the Second and King Abdashart, for those who want to know. But when the Persians decided to attack Phoenician Carthage, things quickly went wrong.

"According to Herodotus," el-Zein says, "the Phoenicians of Sidon refused to build ships for the Persians and help them. And because of this, the Persians never finished their north African project." It makes sense. Why should the Phoenicians of Sidon and Beirut help their masters attack the Phoenicians of Carthage? It would be left to the Romans ("Carthaga delenda est") to destroy the city whose remains lie in modern-day Tunisia and whose land was sown with salt so that it could never be reinhabited.

It's always the same when you think you've got the Lebanese on your side. First they are your friends – the French thought that after the 1914-18 war – and then they become subversive and upset all your military plans, the amiable historical mosquito that bites you when you least expect it and then poisons you. It doesn't hurt until you realise what has happened. Message: leave the Phoenicians/ Lebanese alone. Ask the Israelis.

And so the Persians should have left the Beirutis to their dyeing trade – there are murex shells and wood charcoal aplenty to prove it – and their fishing boats. In the old Roman cities of Europe – in Rome or at Corbridge on Hadrian's Wall – I like to run my hand along the rutted highways of antiquity, where the barrows and horse-drawn carts and chariot wheels of history slowly carved their passage into the great stone Roman roads. Humans didn't just build this; they lived here and travelled here. Those double ruts in the road are fingerprints.

And old Phoenico-Persian Beirut has some "fingerprints" of its own. In the old port, now under rue Allenby – another imperial name, victor of Gaza and humble conqueror of Jerusalem – there is an ancient stone bollard, and cut into it are two natural slits, created during the decades of Persian power. They are the marks worn down by the ropes tying Phoenician ships to the quayside, the stone gradually worn away as the hawsers cut into it, pulled back and forth by the same Mediterranean tide which sloshes away outside my home.