Background Scaffolding is an intermediate stage of fragment assembly. It consists in orienting and ordering the contigs obtained by the assembly of the sequencing reads. In the general case, the problem has been largely studied with the use of distances data between the contigs. Here we focus on a dedicated scaffolding for the chloroplast genomes. As these genomes are small, circular and with few repeats, numerous approaches have been proposed to assemble them. However, their specificities have not been sufficiently exploited. Results We give a new formulation for the scaffolding in the case of chloroplast genomes as a discrete optimisation problem, that we prove to be N P-Complete. It does not require distance information. It is focused on a genomic regions view, with the priority on scaffolding the repeats first. In this way, we encode the multimeric forms issue in order to retrieve several genome forms that can exist in the same chloroplast cell. In addition, we provide an integer linear program to obtain exact solutions that we implement in Python3 package khloraascaf. We test it on synthetic data to investigate its performance behaviour and its robustness against several chosen difficulties. Conclusions While the scaffolding problem is traditionally defined with distances data, we show it is possible to avoid them in the case of the well-studied circular chloroplast genomes. The presented results show that the regions view seems to be sufficient to scaffold the repeats.