Given the high salinity, prevailing annual high temperatures, and ultra-oligotrophic conditions in the Red Sea isolation and characterization of important microbial groups thriving in this environment is important in understanding the ecological significance and metabolic capabilities of these communities. By using a high-­throughput cultivation technique in natural seawater amended with minute amounts of nutrients, members of the rare biosphere (PS1), methylotrophic Betaproteobacteria (OM43), and the ubiquitous and abundant SAR11 group (Pelagibacterales), were isolated in pure culture. Phylogenetic analyses of Red Sea isolates along with comparative genomics with close representatives from disparate provinces revealed ecotypes and genomic differentiation among the groups. Firstly, the PS1 alphaproteobacterial clade was found to be present in very low abundance in several metagenomic datasets form divergent environments. While strain RS24 (Red Sea) harbored genomic islands involved in polymer degradation, IMCC14465 (East (Japan) Sea) contained unique genes for degradation of aromatic compounds. Secondly, methylotrophic OM43 bacteria from the Red Sea (F5, G12 and H7) showed higher similarities with KB13 isolate from Hawaii, forming a ‘H-­RS’ (Hawaii-­Red Sea) cluster separate from HTCC2181 (Oregon isolate). HTCC2181 members were shown to prevail in cold, productive coastal environments and had an nqrA-­F system for energy generation by sodium motive force. On the contrary, H-­RS cluster members may be better adapted to warm and oligotrophic environments, and seem to generate energy by using a proton-­translocating NADH:Quinone oxidoreductase (complex I; nuoA-­N subunits). Moreover, F5, G12, and H7 had unique proteins related to resistance to UV, temperature and salinity, in addition to a heavy metal ‘resistance island’ as adaptive traits to cope with the environmental conditions in the Red Sea. Finally, description of the Red Sea Pelagibacterales isolates from the Ia (RS39) and Ib (RS40) subgroups, principally revealed unique putative systems for iron uptake and myo-inositol utilization in RS39, and a potential phosphonates biosynthetic pathway present in RS40. The findings presented here reflect how environments influence the genomic repertoire of microbial communities and shows novel metabolisms and putative pathways as unique adaptive qualities in diverse microbes encompassing from rare to predominant bacterioplankton groups from the Red Sea.