Nine isolates of unicellular green algae were obtained from six geographically separate desert microbiotic crust communities in western North America. Microscopically, eight isolates strongly resembled unicellular forms of Scenedesmus obliquus (Turpin) Kützing. They are oval or crescent shaped, often flattened on one side, with knobby cell apices. SEM indicated a lack of wall ornamentation. Fine filaments connecting cells pole to pole were observed in some isolates, as previously documented in Scenedesmus (Dactylococcus) dissociatus and S. obliquus. The ninth isolate was spherical, without knobby apices or connections between cells, and was similar to unicellular forms that were originally classified as species of Chlorella (Scenedesmus vacuolatus and S. rubescens). None of the isolates formed coenobia in liquid culture. Phylogenetic analysis of the 18S rRNA gene placed all desert isolates in the genus Scenedesmus, separating them into two or three weakly resolved groups along with published sequences of other Scenedesmus isolates. Phylogenetic analyses of the internal transcribed spacer region revealed well-supported lineages of desert algae that were unsupported with 18S data alone. The eight S. obliquus-like desert strains formed two distinct clades that excluded the S. obliquus strains from geographically widespread nondesert habitats. The ninth strain was outside of the S. obliquus group, associated with S. raciborskii and S. pectinatus. These results demonstrate three lineages of Scenedesmus from desert soils and provide robust support for the presence of cryptic species in S. obliquus, a morphospecies that is said to have a cosmopolitan distribution. Three new species of Scenedesmus are described.