The theory envisaging the origin of plastids from endosymbiotic cyanobacteria is well-established but it is difficult to explain the evolution (spread) of plastids in phylogenetically diverse plant groups. It is widely believed that primordial endosymbiosis occurred in the last common ancestor of all algae^1^, which then diverged into the three primary photosynthetic eukaryotic lineages, viz. the Rhodophyta (red algae), Glaucocystophyta (cyanelle-containing algae) and Viridiplantae (green algae plus all land plants)^2^. Members of these three groups invariably have double membrane-bound plastids^3^, a property that endorses the primary endosymbiotic origin of the organelles. On the other hand, the three or four membrane-bound plastids of the evolutionary complicated Chromalveolates [chromista (cryptophytes, haptophytes, and stramenopiles) and alveolata (dinoflagellates, apicomplexans, and ciliates)] are inexplicable in the light of a single endosymbiosis event, thereby necessitating the postulation of the secondary^4,5^ and tertiary^6^ endosymbiosis theories where a nonphotosynthetic protist supposedly engulfed a red or a green alga^7^ and an alga containing a secondary plastid itself was engulfed^8^ respectively. In the current state of understanding, however, there is no clue about the taxonomic identity of the cyanobacterial ancestor of chloroplasts, even though there is a wide consensus on a single primordial endosymbiosis event. During our metagenomic investigation of a photosynthetic geothermal microbial mat community we discovered a novel order-level lineage of Cyanobacteria that - in 16S rRNA gene sequence-based phylogeny - forms a robust monophyletic clade with chloroplast-derived sequences from diverse divisions of Viridiplantae. This cluster diverged deeply from the other major clade encompassing all hitherto known groups of Cyanobacteria plus the chloroplasts of Rhodophyta, Glaucocystophyceae and Chromalveolates. Since this fundamental dichotomy preceded the origin of all chloroplasts, it appears that two early-diverging cyanobacterial lineages had possibly given rise to two discrete chloroplast descents via two separate engulfment events
