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I know plenty of Japanese words that came from English and a few from other European languages (obviously tons from Chinese), but what about words from Japan's indigenous languages such as Ainu? Also if there are any are they all written in kana like the newer borrowed words?

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Ainu itself is an Ainu word. –  Andrew Grimm Jul 1 '12 at 10:47

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What I think common from them is トナカイラッコ、シシャモ、ノンノ

ref: 日本語に溶け込んだアイヌ語

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I already like "ノンノ" but can't find its meaning other than the name of a women's magazine in Japan. –  hippietrail Jun 27 '11 at 1:30
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@hippietrail, it is flower in ainu language, but popular as magazine name. –  YOU Jun 27 '11 at 1:32

Most Ainu loanwords in regular use are names for plants/animals indigenous to northern Japan, such as reindeer (トナカイ) and sea otter (ラッコ). These loans are old enough that there ARE usually kanji that can be used for them: 馴鹿 (トナカイ, can also be read じゅんろく) 海獺 or 猟虎 (ラッコ)

However, many plant/animal names are usually written in katakana (e.g. カバ for "hippopotamus," though it can be written 河馬) in everyday use. Due to the Ainu words being borrowed so long ago and the fact that many people don't realize they aren't "native" Japanese words, I suspect they are usually written in katakana because of this convention.

I've read in at least a few sources that the word さる "monkey" is from Ainu sar'ush," literally "having a tail." Can't promise it's not a false cognate though. It's treated as a native Japanese word in writing.

Using katakana for loan words was not common practice until after the Meiji restoration (older loans like コーヒ and ガラス can actually be written in kanji, although they generally aren't; たばこ is still written in hiragana).

Aside from that, many place names especially in northern Japan are derived from Ainu. "Sapporo" from Sat-poro-pet and "Shiretoko" from Sir-etok are two off the top of my head. These are generally written in kanji.

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I don't know this for sure, but I believe the word "Kanata" meaning roughly "far away" in Japanese may have come from the Ainu, based on it's homonym by Native Americans, who descended from the Ainu.

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That is a wild theory, for which I haven't been able to find any supporting facts. Do you have any references for this claim? –  Earthliŋ Jul 9 '13 at 14:49
    
What corresponding native American homonym did you have in mind? Kanata? –  Earthliŋ Jul 9 '13 at 23:37

Japanese has also borrowed some words from Okinawan, generally relating to Ryukyuan culture, including:

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There are some words in Japanese which were borrowed from the Ainu language, and mostly, they are written in katakana. However, they are mostly very uncommon words. Likely one of the most common is ラッコ (sea otter) -- I don't know that there is another word for it. Another which you have potentially heard is カムイ, which is analogous to the Japanese 神(かみ).

There may also be words borrowed from the language(s?) of the Ryukyu Islands (e.g. Okinawa), but I am not aware of any specific examples. If there are, they are also likely written (at least mostly) in katakana.

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