Q: So, what's up with this whole Souji/Soushi thing?
A: There is a lot of debate floating around on the web over the given name of Okita. Some say Souji, some say Soushi. This stems from the kanji, which is composed of two characters. The second character can be read either as "shi" or "ji" ("shi" being the more common reading of the two).

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Q: Well then, which is it?
A: Non-english sources overwhelmingly say..... Souji. Let me tell you what I found so you can decide for yourself.

Souji: Toshizo.com has a brief biography on Okita that I have (slowly but surely) been translating. It gives a short story that goes like this: The true reading of the characters for Okita's first name are in fact "Souji", not "Soushi". The reason it has been mispronounced is because in days past, an actor who played Okita in movies was named Jinshi (the character 'shi' being the same as the second caracter in Okita's first name), thus it became so that people, used to Jinshi, said Okita Soushi.
Manga: While manga is not always a reliable source, it is true that when writing about historical characters that authors do some research. In Peacemaker, the furigana (reading of the kanji) over the kanji of Okita's first name read "Souji". This is the same with two other popular Shinsengumi mangas; Burai and Kaze Hikaru.

Kaze Hikaru: In volume 9 of Kaze Hikaru the author tackles this tough question. She says she has looked through many books and done a lot of research on this question, and has found that it is indeed "Souji". During the time of Okita-san's life, he wrote his name a different way (総三)instead of (総司). The reason for the change to(総司)is because sometime between the 1890 and WWII (三)ceased to read "ji". I am trying to get a clear scan of Okita-san's signature to confirm this.

Soushi: This reading is used both on English-language sites, and recognized by most Japanese readers.
Dictionary: If one was to look up the second character of Okita's first name, one would find that the most common pronounciation is "shi". When I showed the character (not the whole name) to my Japanese teacher, I was told it was "shi" (the teacher did not know if the whole name was "shi" or "ji" just by looking at the characters). In fact, "ji" is frequently not even mentioned as a reading!
Around the World: I was informed by Ally, an Okita fan from Spain, that in manga there, Okita's given name is spelled "Soshi"
This thing:

Q:So, what am I supposed to learn from this?
A:To find a source you trust, and go with what they say.