Bacterial secondary chromosomes replicate using mechanisms that reflect their plasmid origins. For example, the replication of chr2 in Vibrio cholerae relies on a plasmid-like origin, ori2, and a specialized regulatory factor, RctB. Importantly, unlike plasmids, the replication of secondary chromosomes occurs only once per cell cycle, which in V. cholerae is achieved by synchronizing the termination of replication with the primary chromosome (chr1). Using genetic mutants, Val et al. showed that this synchronicity is mediated by a checkpoint mechanism, in which the initiation of chr2 replication is triggered by the replication of an RctB binding site on chr1. Chromatin conformation capture data, which revealed physical contacts between chr1 and chr2, suggested that the replication machineries on the two chromosomes are then in close proximity until termination. However, the precise molecular details of the checkpoint mechanism await further characterization.