We conducted studies in May 2013 and June 2014 in Xinjiang to better understand the community structure of microalgae in this area and the impacts of habitational environments on their distribution. The sampling sites were located in different aquatic(lakes, rivers, ditches, ponds, reservoirs) and terrestrial(deserts, meadows, farmlands, shal-lows) habitats in Xinjiang. Two hundred and twenty microalgae samples were collected including 185 water samples and 35 soil samples. Seventy-seven species of terrestrial microalgae were identified, and 9 of them(mainly Cyanophyta and Chlorophyta) were dominant, such as Phormidium, Microcoleus vaginatus, and Chlorococcum humicola. There were 272 of aquatic species, 42 of which were dominant, and the dominant species were a complex of Chlorophyta, Bacillariophyta and Cyanophyta, including Oscillatoria, Phormidium, Scenedesmus, Monoraphidium, Navicula and so on. Compared to the southern warm-temperate extreme arid zone, microalgae species were more abundant in the northern mid-temperate arid zone, especially enriched in shallows, rivers and lakes. According to the multidimensional scaling analysis, terrestrial habitats such as beaches and meadows had similar community structures of microalgae in the same climate zone, while deserts and farmlands had the same community structure in spite of the climate difference. As for the aquatic habitats, there were remarkable differences in the community structure between rivers and other 4 aquatic habitats in the warm-temperate extreme arid zone; in the mid-temperate arid zone, the community structures in the lakes and rivers were similar, but there was a great difference among other aquatic habitats. Our study indicated that different climates and habitational environments may have impacts on microalgae species.