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Two Pyrenopeziza species, P. protrusa and P. nervicola known to have similar morphology, were newly reported from Japan. This study clarified that P. protrusa morphologically differs from P. nervicola in (1) more protruded outermost cells in ectal excipulum, (2) smaller ascospores, and (3) longer and thinner asci. Pyrenopeziza protrusa produces chlamydospore-like brown cells under culture while P. nervicola forms more complex, brown bulbils. These species formed distinct clades based on ITS-5.8S rDNA in the phylogenetic analysis. The two species did not share the same host. • Two Pyrenopeziza species were newly reported from Japan. • The two species produce characteristic structures in culture previously unreported. • The two species were well-defined by barcoding sequences. [ABSTRACT FROM AUTHOR]