聚球藻菌屬（學名：Synechococcus）為聚球藻菌科的一屬藍藻。該屬的模式種為細長聚球藍細菌（Synechococcus elongatus）。
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本屬包括以下物種：
- 銅綠聚球藍細菌 Synechococcus aeruginosus Naegeli 1849
- 可疑聚球藍細菌 Synechococcus ambiguus Skuja 1937
- 紫晶聚球藻菌 Synechococcus amethystinus Copeland 1936
- 弓形聚球藻菌 Synechococcus arcuatus Copeland 1936
- Synechococcus bigranulatus Skuja 1932
- Synechococcus capitatus Bailey-Watts and Komárek 1991[1]
- 雪松聚球藍細菌 Synechococcus cedrorum Sauvageau 1892
- Synechococcus chlorinus (Böcher 1949) Komárek 1970
- Synechococcus diachloros Skuja 1939
- 細長聚球藍細菌 Synechococcus elongatus Nägeli 1849
- Synechococcus endogloeicus Hindák 1996
- Synechococcus epigloeicus Hindák 1996
- Synechococcus intermedius Gardner 1927
- Synechococcus koidzumii Yoneda 1943
- Synechococcus leopoliensis (Raciborski 1910) Komárek 1970
- Synechococcus linearis (Nägeli 1849) Komárek 1976[2]
- Synechococcus lividus Copeland, 1936
- 巨大聚球藍細菌 Synechococcus major
- Synechococcus minutus West 1912
- Synechococcus moorigangae Singh and Bhadury 2019
- 細小聚球藍細菌 Synechococcus parvus
- Synechococcus plancticus Drews et al. 1961
- Synechococcus praelongus Emoto and Yoneda 1940[3]，為Thermostichus praelongus (Emoto and Yoneda 1940) Komárek and Strunecký 2020的異名
- Synechococcus rayssiae Dor 1967
- Synechococcus rubescens Chang, 1980
- Synechocystis spirogyrae Skvortzov 1946
- Synechococcus sublividus Emoto and Yoneda 1940，為Thermostichus sublividus (Emoto and Yoneda 1940) Komárek and Strunecký 2020的異名
- Synechococcus subsalsus Skuja, 1939
- Synechococcus sulfuricus Dor 1967
- Synechococcus vescus Copeland 1936
- Synechococcus viridissimus Copeland 1936
- Synechococcus vulcanus Copeland, 1936
Bailey-Watts AE, Komárek J. [Title pending]. Arch. Hydrobiol. Suppl. 1991; 88:16.
Komárek J. Taxonomic review of the genera Synechocystis Sauv. 1892, Synechococcus Näg. 1849, and Cyanothece gen. nov (Cyanophyceae). Archiv für Protistenkunde 1976; 118:119-179.
Emoto Y, Yoneda Y. Studies on the thermal flora of Japan. 6. Bacteria and algae of the Ibusuki thermal springs. Ecol. Rev. 1940; 6:257-274.
- LPSN - List of Prokaryotic names with Standing in Nomenclature
