聚球藻菌科（學名：Synechococcaceae）為聚球藻菌目的一科藍藻。此科的模式屬為聚球藻菌屬(Synechococcus)。
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本科包括以下屬：
- Aegeococcus Konstantinou and Gkelis, 2021
- Aegeococcus anagnostidisii corrig. Konstantinou and Gkelis 2021，也拼作：Aegeococcus anagnostidisi
- Aegeococcus thuretii Konstantinou and Gkelis 2021，也拼作：Aegeococcus thureti
- Alternantia Schiller, 1954
- Alternantia geitleri Schiller 1954
- Alternantia quadriga Schiller 1954
- Alternantia ramifera Schiller 1954
- Alternantia serra Schiller 1954
- Alternantia tabularis Schiller 1954
- Anathece Cronberg and Komárek, 1994
- Bacularia Borzì, 1905
- Bacularia coerulescens Borzì, 1905
- Bacularia gracilis Komárek, 1995
- Bacularia indurata (Copeland 1936) Frémy 1949
- Bacularia vermicularis Komárek and Anagnostidis, 1995
- Catella Ålvik 1934
- 藍菌屬 Cyanobium Rippka and Cohen-Bazire 1983
- Cyanocatena Hindák 1975
- Cyanocatena bicudoi Ramírez 1996
- Cyanocatena planctonica Hindák 1975
- Cyanocatena verrucosa Hindák 2002
- Cyanodictyon Pascher 1914
- Cyanodictyon balticum Cronberg 2003
- Cyanodictyon endophyticum Pascher 1914
- Cyanodictyon filiforme Komárková-Legnerová and Cronberg 1994
- Cyanodictyon iac Cronberg and Komárek 1994[1]
- Cyanodictyon planctonicum Hickel ex Komárková-Legnerová and Cronberg 1994
- Cyanodictyon reticulatum (Lemmermann 1898) Geitler 1925，基異名：Polycystis reticulata Lemmermann 1898
- Cyanodictyon tropicale Senna et al. 1999，也拼作：Cyanodictyon tropicalis
- Cyanodictyon tubiforme Cronberg 1988
- Cyanodictyon turfosum Lederer 1995
- Cyanogranis Hindák 1982
- Cyanogranis basifixa Hindák 1982
- Cyanogranis ferruginea (Wawrik 1963) Hindák 1982
- Cyanogranis libera Hindák 2002
- Cyanonephron Hickel 1985
- Cyanonephron styloides Hickel 1985
- Cyanothamnos Cronberg 1991
- Cyanothamnos plancticus Cronberg 1991
- Epigloeosphaera Komárková-Legnerová 1991
- Epigloeosphaera brasilica Azevedo et al. 2003
- Epigloeosphaera filamentosa Komárek and Cronberg 2001
- Epigloeosphaera glebulenta (Zalessky 1926) Komárková-Legnerová 1991
- Gibliniella Strunecky and Raabová 2020
- Gibliniella alaskaensis Strunecky and Raabová 2020[2]
- Lauterbornia Pringsheim 1968，為Synechococcus Nägeli 1849的異名
- Lemmermannia Elenkin 1933
- Lemmermannia pallida (Lemmermann 1898) Elenkin 1933
- Lemmermanniella Geitler 1942
- Lemmermanniella flexa Hindak 1985
- Lemmermanniella gracillima Skvortzov 1968
- Lemmermanniella pallida (Lemmermann 1898) Geitler 1942
- Lemmermanniella parva Hindak 1985
- Lemmermanniella terrestris Gama Junior et al. 2012
- Lemmermanniella uliginosa Komárek and Komárkova-Legnerová 2007
- Lithococcus Ercegović 1925
- Lithococcus ramosus Ercegović 1925
- Lithomyxa Howe 1932
- Lithomyxa calcigena Howe 1932
- Maedleria Molinari and Guiry 2021
- Maedleria saprolithica (Mädler 1963) Molinari and Guiry 2021[3]
- Prochlorococcus Chisholm et al. 1992
- 棒條藻屬 Rhabdoderma Schmidle and Lauterborn 1900
- 棒膠藻屬 Rhabdogloea Schröder 1917
- Rhodostichus Geitler and Pascher 1931
- Rhodostichus expansus Geitler and Pascher 1931
- Rhodostichus fluminensis (Fritsch 1929) Bourrelly 1984
- Spirillopsis Naumann 1921
- Spirillopsis irregularis Naumann 1921
- 聚球藻菌屬 Synechococcus Nägeli 1849
Cronberg G, Komárek J. Planktic cyanoprokaryotes found in South Swedish lakes during the XIIth International Symposium on Cyanophyte Research, 1992. Arch. Hydrobiol. Suppl. 1994; 105:337.
Strunecky O, Raabova L, Bernardova A, Ivanova AP, Semanova A, Crossley J, Kaftan D. Diversity of cyanobacteria at the Alaska North Slope with description of two new genera: Gibliniella and Shackletoniella. FEMS Microbiol Ecol 2020; 96:0.
Molinari EA, Guiry MD. [Title pending]. Notulae algarum 2021; 183:2.
- LPSN - List of Prokaryotic names with Standing in Nomenclature
