Cyanobacteria is one of the oldest organisms on earth. It is prokaryotes of oxygenproducing photosynthesis with relatively simple morphology. Jinyang Lake is located in Shanxi Province, which is the largest artificial lake in North China. In this study, five filamentous cyanobacteria were isolated and purified by classical capillary method from algae collected from the water body and shore of Jinyang Lake. Their morphological characteristics (such as cell shape, filamentous width, whether there is sheath) and microstructure were observed by optical microscope, and their phylogenetic relationship were analyzed by 16S rRNA sequence for clarifing the cyanobacteria species in Jinyang Lake. It provided theoretical data for preventing the occurrence of cyanobacteria blooms in lake and maintaining the stability of water resources and environment and ecological balance. The results showed that: (1) the five filamentous cyanobacteria belonged to three families according to morphology, among which two strains of filamentous cyanobacteria were Leptolyngbyaceae (JYH005 and JYH012), two strains were Pseudanabaenaceae (JYH008 and JYH022), and one strain was Desertifilaceae (JYH010). (2) According to the phylogenetic tree based on 16S rRNA sequence, JYH005 was Nodosilinea, and JYH008 was classified as Arthronema, but different morphological characteristics were observed under culture conditions, which may be a new species. JYH010 was a type of Desertifilum. JYH012 was classified as Leptolyngbya. JYH022 was grouped with Pseudanabaenaceae, and the similarity with other cyanobacteria of this family was less than 90%. Therefore, JYH022 belonged to a different genus, so it only was grouped into Pseudanabaenaceae. The research suggested that the morphological identification of the isolated cyanobacteria strains was consistent with the results of 16S rRNA sequence phylogenetic analysis. This study enriched the diversity of filamentous cyanobacteria in Jinyang Lake, Shanxi Province, and provided a certain scientific basis for resource utilization and environmental protection of the lake.