木質醋酸菌最早於1886年由英國釀酒專家阿德里安·約翰·布朗(英語:Adrian John Brown)發表描述,當時名稱為Gluconacetobacter xylinus,後來許多學者將此菌歸入醋桿菌屬,名為Acetobacter xylinum。2012年,木質醋酸菌被歸入新屬駒形桿菌屬中,並為該屬的模式種[2][3]。
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