The genus was first described in 1979,[5][6] and was originally defined to include "small unicellular cyanobacteria with ovoid to cylindrical cells that reproduce by binary traverse fission in a single plane and lack sheaths".

[7] This definition of the genus Synechococcus contained organisms of considerable genetic diversity and was later subdivided into subgroups based on the presence of the accessory pigment phycoerythrin.

[8] Electron microscopy frequently reveals the presence of phosphate inclusions, glycogen granules, and more importantly, highly structured carboxysomes.

Isolates are morphologically very similar, yet exhibit a G+C content ranging from 39 to 71%,[11] illustrating the large genetic diversity of this provisional taxon.

Bergey's Manual (Herdman et al. 2001) now divides Synechococcus into five clusters (equivalent to genera) based on morphology, physiology, and genetic traits.

Cluster 1 includes relatively large (1–1.5 μm) nonmotile obligate photoautotrophs that exhibit low salt tolerance.

[18] More recently, Badger et al. (2002) proposed the division of the cyanobacteria into a α- and a β-subcluster based on the type of rbcL (large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase) found in these organisms.

Moreover, it has been estimated based on molecular dating that the first Synechococcus lineage has appeared 3 billion years ago in thermal springs with subsequent radiation to marine and freshwater environments.

[20] As of 2020, the morphologically similar "Synechococcus collective" has been split into 15 genera under 5 different orders:[21] (gen. nov. means that the genus is newly created in 2020).

[11] Cells are generally much more abundant in nutrient-rich environments than in the oligotrophic ocean and prefer the upper, well-lit portion of the euphotic zone.

[22] In the nutrient-depleted areas of the oceans, such as the central gyres, Synechococcus is apparently always present, although only at low concentrations, ranging from a few to 4×10³ cells per ml.

In the Pacific high-nutrient, low-chlorophyll zone and in temperate open seas where stratification was recently established both profiles parallel each other and exhibit abundance maxima just about the subsurface chlorophyll maximum.

[22] Factors such as grazing, viral mortality, genetic variability, light adaptation, and temperature, as well as nutrients are certainly involved, but remain to be investigated on a rigorous and global scale.

High productivity in coastal river plumes is often associated with large populations of Synechococcus and elevated form IA (cyanobacterial) rbcL mRNA.

[33] Marine Synechococcus species possess a set of genes that function in DNA recombination, repair and replication.