SummaryThe occurrence of the second messenger 3′,5′‐cyclic guanyl monophosphate (cGMP) has been shown in a number of plant species, including barley, tobacco and Arabidopsis. Physiological processes where cGMP signalling has been observed, or has been inferred, to play a role include chloroplast development, α‐amylase production in aleurone tissue, NO‐dependent expression of defence‐related genes and salt/osmotic stress. In most cases, it is unknown how cGMP exerts its effects and what the downstream targets are. A transcriptomics approach was therefore used to identify putative targets for cGMP signalling. Root exposure to 10 μm membrane permeable cGMP induced changes in abundance for many transcripts involved in metabolism, gene transcription, signalling and defence. In particular, monovalent cation transporters such as non‐selective ion channels and cation:proton antiporters were found to be affected in cGMP exposed roots. In addition, exposure to cGMP was found to modulate influx and efflux of the monovalent cations Na+ and K+.