From 2012 to 2016, phytoplankton samples were collected from the Taiyuan section of Fenhe River in the spring, summer and autumn. In this study, a total of five dominant species were identified and morphologically described. Water bloom of Euglena can be found in May, and the dominant species were E. geniculata and E. sanguinea. From July to September, the dominant species became different kinds of Microcystis in different sample sites, including M. aeruginosa, M. novacekii and M. wesenbergii, respectively. A total of eleven strains of bloom-forming algae were successfully isolated. Among them, there were eight M. aeruginosa strains, two M. novacekii strains and one Euglena sanguinea strain. To study the taxonomic status of bloom-forming algae in the Taiyuan section of Fenhe River, phylogenetic analyses based on cpcBA-IGS, gyrB and cpSSU genes were performed from ten isolated strains of Microcystis and one E. sanguinea, respectively. The results indicated that cpcBA-IGS may be a good molecular marker in studying the taxonomy of M. aeruginosa in Fenhe River, and phylogenetic analysis based on cpSSU gene was thought to be effective for understanding relationships among E. sanguinea and the other Euglena species.