知られている限り、全ての藍藻は好気環境下で酸素発生型光合成を行う。ただし、嫌気環境下で非酸素発生型光合成(光化学系Iを使用し、硫化水素を電子供与体として硫黄を生成)を行う例が知られている。また連続暗黒下でも、有機物を利用した従属栄養を行って生育可能な種(通性光独立栄養性)もいる。Synechocystis sp. PCC 6803 など従属栄養能をもつ藍藻は、光合成遺伝子の変異が致死的にならないため(光合成しなくても生きていける)、光合成研究のモデル生物として広く用いられている。またメタゲノム研究(海水などの環境から直接抽出したDNAをもとにしたゲノム解析)から、光合成能を含め代謝的に不完全(光化学系II、ルビスコ、クエン酸回路などの欠失)な藍藻 (UCYN-A, unicellular cyanobacteria group A) の存在が示されているが、これは他生物に共生して栄養的に依存して生きているものと考えられている。古くは「無色の藍藻」が報告されているが、少なくともその一部は全く別の細菌群に属することが明らかとなっている(例: ベッギアトア属)。
ほとんどの藍藻は、クロロフィルa をもつ。一部の藍藻は、クロロフィル a に加えて、クロロフィル b、d、または f をもつ。クロロフィル d や f は生物の中で一部の藍藻のみがもつ色素であり、人間の目には見えない近赤外光を光合成に利用できる。クロロフィル b(または類似色素)をもつ藍藻は、原核緑藻ともよばれる。原核緑藻のプロクロロコックス属 (Prochlorococcus) はクロロフィル a の代わりにジビニルクロロフィル a をもつ点で特異な存在であり、光合成の反応中心でジビニルクロロフィル a を用いる唯一の生物である。またアカリオクロリス属 (Acaryochloris) はクロロフィル a 量が少なく、反応中心でクロロフィル d を用いている。
藍藻の炭素固定はカルビン回路によって行われる。藍藻のもつルビスコ(リブロース1,5-ビスリン酸カルボキシラーゼ/オキシゲナーゼ)には2タイプが知られる。多くの藍藻は、緑色植物などがもつものと相同な Form IB ルビスコをもつ。このような藍藻は β-シアノバクテリア、Form IB ルビスコからなるカルボキシソームは β-カルボキシソーム とよばれる。一方、一部の藍藻(プロクロロコックス属など)は、一部のプロテオバクテリアのものと相同な Form IA ルビスコをもつ(おそらく遺伝子水平伝播による)。このような藍藻は α-シアノバクテリア、Form IA ルビスコからなるカルボキシソームは α-カルボキシソーム とよばれる。
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