Thanks to the development of increasingly powerful sequencing techniques (Roche 454, Illumina, PacBio), work devoted to the study of microbial diversity has undergone extraordinary development during the last decade through metagenomics and single cell genomics. Efficient high-throughput metagenomic data processing chains and genome-based environmental genomic studies now allows for the study of microbial populations and communities in the wild. This has led to a renewal of our view on how microbial assemblage evolve and interact in aquatic environments. In this context, the analysis of 87 Single Amplified Genomes of co-occurring populations of the marine Prochlorococcus HLII ecotype, shed light on how bacterial populations differentiate over time and space through the reshaping of their pan-genome. However, the evolutionary processes that govern the pan-genome dynamics remain controversial.