This is an overview of the larger archaeological sites in Macedonia. Links in bold are the places that in my opinion should not be missed. See here for other places to visit in Macedonia. Click here for hiking in Macedonia and general information about Macedonia.
Heraclea Lyncestis near Bitola, Stobi near the village Gradsko, Bargala near Stip, Golemo Gradiste near Kratovo, Plaosnik in Ohrid, Roman Baths at Bansko, Skupi and the stone aqueduct near Skopje, Antigona near Negotino, Isar Marvinci near Valandovo, Vardarski Rid near Gevgelija.
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