Aim of study: To determine morphological, physiological and molecular responses of cherry rootstocks under salt stress condition. Area of study: Konya, Turkey. Material and methods: A pot trial was conducted to assess moderate salt stress (35 mM NaCl) effects on cherry rootstocks (CAB-6P, MaxMa 14 and Mazzard). We have evaluated many morphological and physiological parameters and analyzed WRKY genes (WRKY25, WRKY33 and WRKY38) under salinity conditions. Main results: All rootstocks survived with slight leaf burn under salinity conditions and the plant growth and physiological parameters, except membrane permeability, decreased in all rootstocks. The membrane permeability increased with salinity and the lowest increment in the membrane permeability (12.17%) was in MaxMa 14, while CAB-6P and Mazzard showed higher levels of increases reaching 46.81 and 56.42%, respectively. Furthermore, the expression of WRKY25, WRKY33 and WRKY38 genes was significantly increased by salinity. The rankings of the WRKY genes expression levels among control rootstocks were: MaxMa 14 < CAB-6P < Mazzard. Research highlights: CAB-6P, MaxMa 14 and Mazzard rootstocks were found relative salt-tolerant at the moderate salinity levels and there is a cross-talk between physiological and molecular responses. Mazzard had higher tolerance to salinity shown in molecular responses. The study possesses importance for plant physiologists and cherry growers as it showed how cherry rootstocks respond to salt stress.