The genome of bacteria is classically separated into the essential, stable and slow evolving chromosomes and the accessory, mobile and rapidly evolving plasmids. This distinction has been blurred in recent years by the characterization of multipartite genomes constituted of a primary "standard" chromosome and one or several additional and essential replicons adapted to the cell cycle. Depending on the authors, these genomic elements are either named "secondary chromosomes" or "megaplasmids". However, their true nature and evolution are yet to be determined. Here we investigate the relationships of these secondary essential replicons (SERs) to classical chromosomes and plasmids based on the key processes involved in the maintenance of genomes and replicons, i.e., their replication, partition and segregation, and perform a global comparative genomic analysis for all bacterial replicons available from public databases. Several classes of replicons could thus be characterized, and chromosomes, plasmids and SERs differentiated. This sets the basis to the investigation of the emergence of SER-like genomic structures.