After the conversion from farmland to forest of northern Shaanxi Province in Loess Plateau, biocrust has become a typical surface cover type, which is rich in soil algae and plays an extremely important role in fixing soil and promoting nutrient cycling. In this study, soil algae of northern Shaanxi in Loess Plateau were isolated and cultivated by coating plate method and water droplet dilution method. Morphological characteristics of microalgae were observed by optical microscope, and molecular identification of single algae was carried out, which laid a foundation for the study of biocrusted algae of northern Shaanxi in Loess Plateau. The results showed that: (1) a total of 7 species of crusted algae were purified and identified by optical microscopy, among which 5 were green algae and 2 were cyanobacteria. (2) The sequence lengths of five green alage strains of SM21, DB21, DB22, SD1 and SD2 were 664 bp, 663 bp, 662 bp, 589 bp and 688 bp, and GC contents were 33.43%, 49.47%, 50.15%, 50.76%, 51.01%, respectively; The sequence lengths of YJ3 and YJ2 strains of cyanobacteria were 570 bp and 465 bp, and GC content was 46.31% and 49.03%, respectively. (3) Sequence alignment and phylogenetic tree analysis showed that the 5 green algae could be divided into four clades: Scenedesmaceae (2 strains: DB21 and SM21), Chlamydomonadales, Shaeropleaceae and Eustigmataceae, respectively. And the 5.8S+ITS2 sequences of the 5 green algae showed little difference within the genus and were very conservative, which made it easy to identify the genus. 2 strains of cyanobacteria, YJ3 and YJ2, were clustered in the same big branch of Pseudanabaenaceae, but they belonged to different genus. The research suggests that DB21 was a species of Scotiellopsis, SM21 belonged to Acutodesmus, DB22 belonged to Haematococcus, SD1 was a species of Ancyra, and SD2 belonged to Eustigmatos.YJ3 may be a new species of Pseudanabaenaceae, and YJ2 may be a new species of Leptolyngbya.