Cyanobacteria are prokaryotes (single-celled organisms) often referred to as "blue-green algae." While most algae is eukaryotic (multi-celled), cyanobacteria is the only exception. Cyanobacteria obtain their energy through photosynthesis. They are not strictly unicellular, but can be found in colonial and filamentous forms, some of which differentiate into varying roles. For example, cyanobacteria specialized for nitrogen fixation are called heterocysts.

Cyanobacteria are very old, with some fossils dating back almost 4 billion years (Precambrian era), making them among the oldest things in the fossil record. They played a key role in increasing the amount of oxygen in the Earth's atmosphere. For almost 2 billion years, cyanobacteria and other prokaryotes were the only organisms on Earth, eukaryotes not having evolved yet. Conceivably, life on other plants, if it exists, may consist of prokaryotes and no eukaryotes. Due to their simplicity, prokaryotic cells are about 1000 times smaller than eukaryotic cells.

Unlike most organisms which use photosynthesis for energy, cyanobacteria carry out photosynthesis directly in the cytoplasm of the cell, rather than in specialized organelles (chloroplasts). In fact, the chloroplasts found in all plants are probably evolved cyanobacteria. Considering that cyanobacteria possess their own DNA, it is theorized that more sophisticated plant cells brought cyanobacteria into their structure through the initiation of an endosymbiotic relationship.

Cyanobacteria lack cilia, performing locomotion by gliding along surfaces. They are found most frequently in freshwater, but variants exist almost anywhere where there is water, including inside of other organisms such as lichen, plants and protists. Cyanobacteria possess thick cell walls to protect them from the outside and preserve homeostasis.

Photosynthesis in cyanobacteria uses water as an electron donor and produces oxygen as a byproduct. The photosynthesis occurs in membranes called thylkoids, with chlorophyll being employed to absorb the sun's rays. Unlike most photosynthetic organisms, cyanobacteria are blue-green or grayish-brown in color rather than plain green.

Based on their shapes (morphologies), cyanobacteria have been classified into five groups: chroococcales, pleurocapsales, oscillatoriales, nostocales and stigonematales. Based on actual phylogenetic studies, the common lineage of only the last two groups has been established. Just because two organisms have a similar shape, they are not necessarily phylogenetically related, members of the same classificatory group known as a phylum.