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Borrowed from Okinawan蛇(habu, “snake”). Likely cognate with Japanese蛇(hebi, “snake”).
Possibly an alteration from 反鼻(hanbi), an obsolete term for a kind of Chinese medicine made from the skin and/or organs of certain venomous snakes.
More likely, may be an alteration from 蛇(hebi, “snake”). Some dialects distinguish between non-poisonous hebi and poisonous habi.
Possibly also related to, or influenced by, Old Japanese-derived verb 食む(hamu, “to bite”). An /m/ - /b/ alternation can be found in some Japanese words, so a shift from hamu to habu is a reasonable possibility. The standard modern Japanese word hebi for “snake” may similarly be derived from, or have been influenced by, hamu “to bite”.
The kanji spelling 波布 is an example of ateji, with the characters chosen purely for their phonetic values.
As with many terms that name organisms, this term is often spelled in katakana, especially in biological contexts (where katakana is customary), as ハブ.