The men, ages 28 and 19, were travelling by bus to Turkey when they were arrested in Alexandroupolis near the Turkish border.
AFP write that police found two machetes, army uniforms and other "combat paraphernalia" inside the pairs luggage.
Police charged both with carrying weapons and are expected to appear in court on Tuesday.
The 28-year-old is Bosnian-born and reportedly known to European authorities for his ties to jihadist groups. He's also been convicted for planning a terrorist attack and was under the close eye of Swedish authorities, police sources told AFP.
AFP writes that the men landed in Greece from Sweden "10 days ago", and they traveled by bus to Thessaloniki and then to Alexandroupolis.
Swedish Foreign Ministry confirmed that two Swedish citizens were arrested in Greece and being held for weapons crimes, according to Swedish Radio News.