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The distribution and diversity of the waterbloom-forming cyanobacteria, mainly including Microcystis species, were investigated using molecular approaches in Lake Ulungur, an increasingly eutrophic and brackish lake located in Xinjiang, China. Real-time PCR analyses showed the abundance of Microcystis 16S rDNA gene copies in the Ulungur Lake is low, at 7.2 x 10(4) copies L (-aEuro parts per thousand 1) averagely and 4.5 x 10(5) copies L (-aEuro parts per thousand 1) at maximum. Two Microcystis species, M. aeruginosa (Kutzing) Lemmermann and Microcystis wesenbergii (Komarek) Komarek were, for the first time, reported in this lake. The mcyA gene-specific PCR determination on the isolates of Microcystis showed that the M. aeruginosa strains are all mcyA-containing genotypes, while M. wesenbergii are non-mcyA-containing ones. The microcystin contents of the toxic M. aeruginosa strains were shown to be lower than those of the Microcystis strains isolated from other eutrophic lakes in China. Phylogenetic analyses based on 16S rRNA and rpoC1 genes showed that the Microcystis strains isolated from the Ulungur Lake were not genetically divergent from those isolated in the other freshwaters. Such an investigation would contribute to the knowledge on the bloom-forming cyanobacteria of the increasingly eutrophic and saline lakes in the desert area.