The Taiyuan region of the Fenhe River is a large park with a theme of "people, city, ecosystem and culture", which promotes relaxation, vacationing and sightseeing. This portion of the river is approximately 12 km in length, 500 m in width and covers an area of 600 hm². In recent years, the influx of domestic and industrial sewage in the upper reaches of the Fenhe River has caused the self-cleaning capacity of the river to deteriorate, degraded the river's water quality and enhanced eutrophication in the water body. Subsequently, sensitive species of phytoplankton have dramatically reduced, resulting in a decline in the river's diversity index and a more simplified community structure, which is prone to cyanobacteria blooms. To date, more than 60% of the lakes in China have been subject to eutrophication and have suffered from cyanobacteria blooms. Microcystis is the most frequently reported cyanobacteria genus. It has long been a primary focus of attention because of its potential to produce microcystins and to cause an undesirable taste and odor in freshwater sources. In 2011, the section of river in Taiyuan was subject to an unprecedented cyanobacteria bloom over a large area. While the affected waters spanned a length of several kilometers, the area between the Yingze Bridge and the Nanneihuan Bridge was the most seriously affected. To control eutrophication and prevent the recurrence of blooms, phytoplankton diversity and the presence of odorous compounds produced by Microcystis were investigated in the Taiyuan region of the Fenhe River. The water quality assessment was based on data collected during July and October, 2012. A total of 126 phytoplankton species belonging to 65 genera and 6 divisions were identified. Among these, the Chlorophyta was the most dominant division, including 57 species from 25 genera, followed by Bacillariophyta, with 40 species from 26 genera, Cyanophyta with 20 species from 9 genera, Euglenophyta, with 5 species from 2 genera, Dinophyta with 2 species from 2 genera and Cryptophyta, with 2 species from a single genus. The dominant species in July 2012 comprised Merismopedia tenuissima and Microcystis incerta (Cyanophyta), Synedra acus (Bacillariophyta), Scenedesmus quadricauda and Dictyosphaerium pulchellum (Chlorophyta), Peridinium pusillum (Pyrrophyta). In October 2012, the prevalent species were Merismopedia tenuissima, Planktothrix agardhii and Oscillatoria amphibia (Cyanophyta), Synedra acus (Bacillariophyta), Scenedesmus quadricauda (Chlorophyta), Cryptomonas erosa (Cryptophyta) in October, 2012. The average cell densities of phytoplankton were 188.28×10⁶ cells/L and 58.66×10⁶ cells/L at the Yingze Bridge area in July and October 2012, respectively. Meanwhile, the average cell densities of phytoplankton were 83.78×10⁶ cells/L and 65.99×10⁶ cells/L at the Nanneihuan Bridge area in July and October, 2012, respectively. This indicated that the water body was eutrophic. The Margalef index ranged from 2.04 to 2.68, and the Shannon-Wiener index ranged from 0.49 to 1.00 and the Pielou evenness index ranged from 0.13 to 0.26 at this location. These three indices revealed that the water quality was medium to heavy polluted. Eight purified Microcystis strains were isolated from the samples, and their volatile odorous compounds were determined by gas chromatography and flavor analysis. Among these, six strains were found to produce the odorous compound β-cyclocitral. The presence of these problematic species and the resulting compounds highlight the need to improve the water quality in the Taiyuan section of the Fenhe River, to prevent the recurrence of blooms.