The order Endogonales within Mucoromycotina includes several ectomycorrhizal species and endophytes of lower land plants. As such, this order is a key taxon for investigation of the evolutionary process of plant–fungal symbioses. However, no taxonomic study of Endogonales based on morphological and phylogenetic data has been performed, and the geographic distribution of this order in Asia remains largely unknown. We collected E. incrassata, E. pisiformis, E. flammicorona, and E. lactiflua from forests in Japan, thus representing their first description in Asia. Collected sporocarps were examined microscopically to observe details of hyphal structures, particularly in zygosporangia and gametangia. In addition, we collected Japanese Sphaerocreas pubescens, recently reported to be related to Endogone-like mycobionts of liverworts, and described its morphology. Species were also analyzed phylogenetically based on large-subunit nuclear ribosomal RNA gene sequences. The phylogenetic relationships of the four Endogone species were supported by their zygosporangial morphogenesis: group A, comprising E. incrassata and E. pisiformis, formed homogametic zygosporangia with pale-colored sporangiothecia, whereas species in group B, E. flammicorona and E. lactiflua, formed heterogametic zygosporangia with orange-colored sporangiothecia. Sphaerocreas pubescens was phylogenetically close to Densospora solicarpa, which is an uncertain zygomycotan ectomycorrhizal fungus; however, the relationship between the “Sphaerocreas/Densospora” clade and Endogone was unclear. © 2015, German Mycological Society and Springer-Verlag Berlin Heidelberg.