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Looking on Wikipedia I see that in many of the languages of the former communist countries, namely East European, the North Korean leader Kim Il Sung (or Song) (1912-1994) is called Kim Ir Sen. (I am posting the Polish page because it has more links to other languages than other pages have.)

The difference is not in the family name - which is Kim.

It seems a difference based on the former political divide of the Cold War, as in French and other West European languages, but also in Turkish and Greek (Turkey and Greece already being NATO members at the time), the name used is the same as in English. On Wikipedia I have not found a non (former) communist country that calls him Kim Ir Sen.

I see no linguistic similarity between countries using the same form of the name (Russian, Latvian, Albanian, Romanian share the same "communist" form), so the cause must be politic. But how has been the political divide projected in the name of this man?

To make things more interesting, there are also some exceptions: in former-Yugoslav countries, that is on the Wikipedia pages in Serbian, Croat, Slovenian and Macedonian, he is called like in the Western Europe: Kim Il Sung.

In Bulgarian, which is close if not identical to Macedonian, it's Kim Ir Sen. At least Croats and Serbs use the same name... But not Slovak and Czech, which were in the same country during the communist era: the Wikipedia page in Slovakian uses the "Western" form.

Maybe this differences between neighbours are recent. Are they also political?

The difference in pronunciation between "Ir Sen" and "Il Song" may be bigger in some languages than in others. In some languages it seems big to me (French, Romanian); maybe it's less striking in English... This is even more confusing by the fact that the Kim dynasty includes already three names of presidents all called Kim, a series in which the aforementioned difference might suggest a fourth one.

Under an older system of transliteration, the Russians transliterated 김일성 (Kim Il-Sung) as Ким Ир Сен (Kim Irsen), which is still the standard way of rendering his name in Russian. Under the currently standard Kontsevich system, it would instead be transliterated as Ким Ильсо́н (Kim Ilson).

It seems that those countries that were closer to Russia politically tended to follow the Russian transliteration Ким Ир Сен (Kim Irsen); while those more to the west tended to use the Roman transliteration Kim Il-Sung.

By the way, this explains why Kim Jong-Il (son of Kim Il-Sung) was born Yuri Irsenovich (son of Ir Sen) Kim.

See this discussion: https://thediacritics.wordpress.com/2012/01/03/whats-in-a-kim/

The Korean language has a different set of phonemes compared to most Indo-European languages.

Phonemes are individual sounds that are distinguished in pronunciation and used to differentiate words. For example, in English the words lot and rot are perceived as different because of the way the first letter (l versus r, typically denoted /l/ versus /r/) is pronounced. The East Asian languages Korean and (perhaps more famously) Japanese do not distinguish between an /l/ and an /r/ sound. In the Korean script, these both correspond to one letter (ㄹ). Depending on the surrounding, this sound may sound more like an l or more like an r to a westerner but a Korean will ‘hear’ no significant difference.

Furthermore, the vowel in Sung, denoted in Korean by the symbol ㅓ, corresponds to a sound which does exist in most European languages but does not have its own reserved letter: the schwa sound (again with potentially different pronunciation depending on the environment). In English, the schwa is used for reduced vowels: the e in unemphasised the, the second o in common or others. Korean uses a single symbol and differentiates it from other vowels such as a, e, i, etc.

The differences are suddenly significant when one tries to transliterate the original Korean into another language with a different script. Maybe you have seen the different spellings of Mao (Mao Tse-tung or Mao Zedong) depending on which romanisation standard was used. Likewise, various methods for the transliteration of Korean exist which were used at different times and by different countries.

According to the currently used system of South Korea (Revised McCune-Reischauer), the name would be spelt Kim Il-Seong in English—a spelling you probably have never seen before. The previous romanisation would indeed have turned him into the more common Kim Il-Sŏng. Because it was used at the time, people got used to it and the name was not changed when the revised system was introduced.

Unfortunately, I am not able to exactly source what happened in these countries you mention. However, the other answer has already provided that a different, older transliteration system was used in Russian. Russian, using Cyrillic letters, again needs to be transcribed into the Latin alphabet for languages such as Polish or Latvian which creates two levels of abstraction if the Russian spelling was used as the starting point—considering the history of these countries post World War II (when Kim Il-Song was contemporary) seems likely. As I mentioned above, the Latin and Korean alphabets don’t provide a perfect mapping—much worse than e.g. Latin and Cyrillic—so minor differences will occur and be carried on without there being any reason to assume a political background.

A case in point for a different script pair is the name of the last leader of the Soviet Union, rendered Gorbachev in English but Gorbatschow in German (East and West)—note the difference e versus o in the final syllable.