With Cyprus being so bitterly divided, it comes as no surprise to find that a bit of geographical revisionism has been going on. This is particularly prevalent in the north, where all Greek writing has been obliterated from signposts, and place names have officially been changed to reflect the Turkish occupation of that part of the island. It means that places in northern Cyprus can have a number of different names, depending on whom you ask.
In the south the place names haven't changed, but things are just as confusing for foreigners, as the southern part of the island uses the Greek alphabet, which doesn't have an exact transliteration into the Roman alphabet at the best of times (for example the letter γ is sometimes like a 'y' and sometimes like a 'g', and the letter π is often a 'p' but also, at times, a 'b'). To make things even more confusing, the Cypriot government adopted an EU-recommended transliteration scheme in 1994 that totally changed the way Cypriot place names are written in the Roman alphabet. By all accounts the Cypriots themselves aren't terribly impressed with the new versions, even though their road signs have almost all changed to the new scheme; however, foreigners really have a problem with the new system, as the previous names were relatively phonetic, unlike the new ones.
One good example is Agia Napa, which was known as Ayia Napa before 1994 (and that's how you pronounce it, as the γ after the Α in Αγια is pronounced as a 'y' in this case). Another cracker is Lefkosia, which used to be known as Nicosia; in this case those behind the change felt that Nicosia was a hangover from British rule (despite the fact that the name was adopted by the Lusignans), so the change to the Greek version of Lefkosia wasn't so much to do with transliteration as nationalism.
So what's a writer to do? Well, I started writing these articles with a modern map in front of me, and therefore I've ended up using the new versions, even though most UK tour operators, Friends of the Earth, some guidebook publishers and a number of important international organisations have decided to ignore the new scheme and stick to the old versions. The only place where I use the old version in preference is in the article on Nicosia, because nobody I've met uses the new version, and the internationally accepted name for the city is still Nicosia. Where possible I've pointed out the previous spelling in a footnote, but that's about as much as anyone can do without including the old name in brackets every time, and that would make it unreadable.
Still, Cyprus isn't the first country with variable spelling, and it won't be the last, so it's not worth getting in a strop...