Calcineurin B-like protein interacting protein kinases (CIPKs) are key regulators of pre-transcriptional and post-translational responses to abiotic stress. Arabidopsis thaliana CIPK16 (AtCIPK16) was identified from a forward genetic screen as a gene that mediates lower shoot salt accumulation and improved salinity tolerance in Arabidopsis and transgenic barley. Here, we aimed to gain an understanding of the evolution of AtCIPK16, and orthologues of CIPK16 in other plant species including barley, by conducting a phylogenetic analysis of terrestrial plant species. The resulting protein sequence based phylogenetic trees revealed a single clade that included AtCIPK16 along with two segmentally duplicated CIPKs, AtCIPK5 and AtCIPK25. No monocots had proteins that fell into this clade; instead the most closely related monocot proteins formed a group basal to the entire CIPK16, 5 and 25 clade. We also found that AtCIPK16 contains a core Brassicales specific indel and a putative nuclear localisation signal, which are synapomorphic characters of CIPK16 genes. In addition, we present a model that proposes the evolution of CIPK16, 5 and 25 clade.