The tenfold dilution method was used to isolate and purify the desert microalgae from the sand samples that collected from the Yuli County, Xinjiang; and the 18S rDNA gene was used for molecular analysis of the isolates; the morphological characteristics of 5 microalgae were observed using light, scanning and transmission electron microscopy. Moreover, the biochemical content of the 5 microalgae was also determined. The results indicated that: (1) total of 23 microalgae were isolated; and the phylogenetic tree inferred based on the 18 rDNA gene showed that those isolates were the members of five different genera, Chlorosarcinopsis, Marvania, Chlorella, Protosiphon and Chlamydomonas respectively, among which the number of species belong to Chlorosarcinopsis was occupied 60.87% of all isolates. (2) The growth curve of the five species was indicated “S” shape and their optimum growth temperature was around 25-35℃. (3) The biomass of the five strains were all lower than that of control group (CC127); whereas, the total protein content was higher than that of CC127, except XLDM4, and the protein content of the four strains，XLDB4, XLDB6, XLDB9, XLDM5，were equivalent to 1.57, 2.13, 1.07, 1.21 times of the control group, respectively. The fatty acid content of those five species mainly comprised of unsaturated fatty acids, among which the 18C unsaturated fatty acid (linoleic acid / isooctadecanoic acid) is the highest, 44.88% in XLDB9; and 16C saturated fatty acid was in the second place which was 37.88% in XLDM4. This study provides a reference for the development and application of microalgae resources in extreme environments and the preliminary discussion on the geology and ecological environment evolution of Taklamakan desert.