The dataset contains sequence information of the historical biogeographic study of the plant family Zygophyllaceae in the Atacama Desert. We provide three nexus files containing chloroplast sequence data used for all phylogenetic divergence time estimation analysis of the paper. The first nexus file (Zygophyllales_CP_Master.nex) contains the concatenated sequence alignment with character set annotations for the three-chloroplast marker (rbcL, trnL-trnF, trnS-trnG) as well as for hotspot regions and sequence inversions which were excluded and reverse complemented for analysis. The second nexus file (Zygophyllales_CP_Master_HSEX_INVREV_BEAST.nex) is identical to the first one except from the fact that all hotspot regions were excluded and the inversions reverse complemented. This dataset was used for the dating analyses. The third nexus file (Zygophyllales_CP_Master_HSEX_INVREV_RAxML.nex) was used for the phylogenetic reconstruction using a Maximum Likelihood approach. Finally, we provide the R-skript used to plot the time calibrated trees and the ancestral area reconstruction.