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The Gobi Desert in Mongolia, home to the critically endangered Gobi bear (Ursus arctos isabellinus), has few water resources for the animals that inhabit this environment. The majority of these water resources are shallow, small bodies of water, from approximately 30 cm to 3 m in diameter. Due to the harsh nature of the Gobi Desert environment, such pools of water are crucial resources for wildlife inhabiting the area and little information is currently available on the presence of organisms, including cyanobacteria, and the toxins they produce within these waters. Drinking water sources and small pools within the Gobi Desert were sampled on two separate occasions in October 2008 and April-May 2009. Samples were assessed for the presence of cyanobacteria; subsamples were taken for the analysis of beta-N-methylamino-L-alanine (BMAA) and 2,4-diaminobutyric acid (DAB). According to LC-MS/MS analyses, both of these neurotoxic amino acids were present in both years and BMAA was present when cyanobacteria were major components of the pools. The results indicate that assessment of cyanotoxins to organisms that live in desert environments is warranted.