Abstract Glomeraceae is the first described and the largest family of the Glomeromycota, currently comprising almost 50% of all species and ca. one-third of all genera hitherto attributed to this phylum. In the Glomeraceae, the genera are separated based on phylogeny and generally present a difference ≥ 10% in the maximum identity (MI) on the partial nrDNA gene. Based on the phylogeny for the partial nrDNA gene, the genus Septoglomus clearly separates into different generic clades. Thus, the present study aims at separating species of the genus Septoglomus respective the “Septoglomus species complex/clade,” based on three leading species Septoglomus constrictum, S. deserticola, and S. viscosum. Septoglomus viscosum is a homotypic synonym of Viscospora viscosa, whose basionym is Glomus viscosum. The basionym of S. deserticola is Glomus deserticola. In this study, a new genus, namely, Blaszkowskia, is described based on B. deserticola, and V. viscosa is formally transferred from the Entrophosporaceae to the Glomeraceae. It has become difficult to separate the genera based on the morphology of members of the Glomeraceae. However, Septoglomus species, also those with relatively small spores, have generally constricted subtending hyphae, and the subtending hyphal pores are regularly closed by a strong septum or a more prominent “plug closure.” Viscospora viscosa has generally pronounced funnel-shaped to cylindric subtending hyphae and a large septum that resembles the pore closures in the subtending hyphae of Funneliformis species. Moreover, V. viscosa spores are significantly smaller than those of Funneliformis and Septoglomus species and are, so far, known exclusively without pigmentation. Finally, B. deserticola has slightly funnel-shaped subtending hyphae and short, fine septa in the subtending hyphae, while the hyphae are pronounced pigmented over a long distance of > 100 μm, which is not known for Viscospora or Septoglomus species, not even in spore clusters. The first key for the morphological identification of the genera within the family Glomeraceae is presented in the current study.