During independent surveys of freshwater ascomycetes in Japan and USA two new species of Lindgomyces were collected from submerged wood in freshwater. These species are described and illustrated based on morphological data and phylogenetic relationships based on analyses of nuclear ribosomal sequence data (partial SSU and LSU, and ITS). Lindgomyces apiculatus, collected in Japan, is characterized by immersed to erumpent, globose to subglobose ascomata; fissitunicate, cylindrical to clavate asci; and fusiform, one-septate ascospores with acute ends and short terminal appendages. Lindgomyces lemonweirensis, collected in Wisconsin, USA, differs from L. apiculatus in having clavate to cymbiform asci and oblong to fusiform ascospores that are distinctively multiguttulate and surrounded by an oval, ephemeral gelatinous sheath. The new species formed a strongly supported clade within the family Lindgomycetaceae (Pleosporales, Dothideomycetes) based on analyses of combined SSU and LSU sequence data. In addition phylogenetic analyses with ITS sequence data support the establishment of the new taxa as separate species within Lindgomyces because they were separated from each other and other Lindgomyces species based on maximum likelihood bootstrap and Bayesian analyses.