TheZygophyllumandTetraenagenera are intriguingly important ecologically and medicinally. Based on morphological characteristics,T. hamiensisvar.qatarensis,andT. simplexwere transferred fromZygophyllumtoTetraenawith the least genomic datasets available. Hence, we sequenced theT. hamiensisandT. simplexand performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp—typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in bothTetraenaspecies. An unusual shrinkage of IR regions 16–24 kb was identified. This resulted in the loss of 16 genes, including 11ndhgenes which encode the NADH dehydrogenase subunits, and a significant size reduction ofTetraenaplastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes,matK,rbcL, andcssAgenes exhibited identical topologies, indicating that both species are sisters to the genusTetraenaand may not belong toZygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence ofZygophyllumandTetraenawas 36.6 Ma and 34.4 Ma, respectively.Tetraenastem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely relatedTetraenaandZygophyllumspecies. It can be potentially used as a universal super-barcode for identifying plants.