Synechococcus, a genus of unicellular cyanobacteria found throughout the global surface ocean, is a large driver of Earth’s carbon cycle. Developing a better understanding of its diversity and distributions is an ongoing effort in biological oceanography. Here, we introduce 12 new draft genomes of marine Synechococcus isolates spanning five clades and utilize ~100 environmental metagenomes largely sourced from the TARA Oceans project to assess the global distributions of the genomic lineages they and other reference genomes represent. We show that five newly provided clade-II isolates are by far the most representative of the recovered in situ populations (most ‘abundant’) and have biogeographic distributions distinct from previously available clade-II references. Additionally, these isolates form a subclade possessing the smallest genomes yet identified of the genus (2.14 +/- 0.05Mbps; mean +/- 1SD) while concurrently hosting some of the highest GC contents (60.67 +/- 0.16%). This is in direct opposition to the pattern in Synechococcus’s nearest relative, Prochlorococcus – wherein decreasing genome size has coincided with a strong decrease in GC content – suggesting this new subclade of Synechococcus appears to have convergently undergone genomic reduction relative to the rest of the genus, but along a fundamentally different evolutionary trajectory.