CetZs are tubulin superfamily cytoskeletal proteins unique to the archaea and have known roles in the control of cell shape and motility. CetZ1, the most conserved CetZ homologue, is essential for rod cell shape development in the pleomorphic archaeon Haloferax volcanii and is important for motility and the assembly and positioning of the archaellum and chemosensory arrays. In this study, we report the function of the paralog CetZ2 as a stationary phase-specific protein that contributes to maintenance of plate cell shape. High resolution fluorescence microscopy revealed that CetZ2 subcellular assembly and dynamics are growth-phase specific and highly active in mid-stationary phase. At this stage, CetZ1 and CetZ2 dynamic assemblies were specifically dependent on one another and their GTPase functions, which suggested that CetZ2 operates by inhibiting the rod-promoting function of CetZ1. The impact of CetZ2 on CetZ1 assembly and function was specific to stationary phase, implying that additional stationary-phase factors are involved. CetZ1 and CetZ2 thus coordinate to control cell morphogenesis in the growth cycle in response to starvation or related environmental cues as culture conditions change. CetZ1 and CetZ2 are co-conserved in many haloarchaea, indicating that their coordinated functions are likely to be widely utilized to control dynamic morphogenesis. Our findings show that CetZ paralogues can have distinct and non-redundant functions, and that diversification and specialisation within the tubulin superfamily has occurred multiple times in archaeal evolution.