Microalgae cultivation has recently been recognized as an important issue to deal with the increasingly prominent resource and environmental problems. In this study, desert cyanobacterium Microcoleus vaginatus was open cultivated in 4 different cultivation conditions in Qubqi Desert, and it was found Chlorella sp., Scenedesmus sp. and Navicula sp. were the main contaminating microalgal species during the cultivation. High light intensity alone was responsible for the green algae contamination, but the accompanied high temperature was beneficial to cyanobacterial growth, and the maximum biomass productivity acquired was 41.3 mg L-1 d(-1). Low temperature was more suitable for contaminating diatoms' growth, although all the microalgae (including the target and contaminating) are still demand for a degree of light intensity, at least average daily light intensity >5 mu E m(-2) s(-1). As a whole, cultivation time, conditions and their interaction had a significant impact on microalgal photosynthetic activity (Fv/Fm), biomass and exopolysaccharides content (P < 0.001). (c) 2015 Elsevier Ltd. All rights reserved.