Hydropunctaria nipponoamphibia is a species of lichen-forming fungus in the family Verrucariaceae. Hydropunctaria nipponoamphibia was described as a new species in 2024 by Hiroshi Harada and Kojiro Hara. The species epithet nipponoamphibia combines nippono-, meaning Japan, with amphibia, meaning "living both in water and on land". The name alludes to the species' resemblance to Hydropunctaria amphibia. The holotype (specimen CBM FL-41444) was collected by Harada and collaborators on 31 August 2019 from seaside rock at Iwadate-tsuka-no-dai, Hachimori, Happou-cho, Yamamoto-gun, Akita Prefecture, Honshu, Japan, at an elevation of 0.5 m.
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