As hearsay has it, both versions are made from strains of Basma, an "Oriental" tobacco plant with it's roots around the Med. Cyprian leaf starts as a type named Smyrna. I believe the Syrian strain is called Shek-el-Bint, or something like that. The other difference is in the materials they use to smoke the leaves in their barns. In Cyprus, they use evergreen bushes and trees, with perhaps some local sages. The Syrians used different stuff, like an oak that as I understand it was going extinct and is now protected as a species. I am also told that some other sages and scrub were added as well, though the details are sketchy at best. Short of getting a hold of an old tobacco grower, this is all we have, guess work, rumour, and history.
I've tried blends with each type of Latakia in them, and they are quite different from each other, in that (I think) the Cyprian, using evergreens, has a sharper bite to the smoky flavor, whereas the Syrian tends to be softer on the palette.
I have also taken it upon myself to have a bowl of the Cyprian solo, to taste the full effect to help me imagine it's place in my blends.
Probably won't do that again.
Though I do wish I could get a bowl of the Syrian, just so I could say I tried it...