In this work, we analysed the natural variation in mechanisms for protection against salt stress in pepper varieties (Capsicum chinense Jacq. cv. Rex, Chichen-Itza and Naranja and Capsicum annuum L. cv. Padron), considering primary root growth and viability of the post-stressed seedlings. NaCl-induced K+ and H+ efflux in roots was also studied by ion-selective microelectrodes under application of pharmacological agents. In these pepper varieties, the magnitude of the K+ leakage in the roots positively correlated with growth inhibition of the primary root in the presence of NaCl, with Rex variety showing a higher level of tolerance than Chichen-Itza. The K+ leakage and the activity of the H+ pump in the roots were dependent on the NaCl concentration. Pharmacological analysis indicated that the NaCl-induced K+ leakage was mediated by TEA+-sensitive KOR channels but not by NSCC channels. In addition, we present evidence for the possible participation of proline, and a Na+-insensitive HAK K+ transporter expressed in habanero pepper roots for maintaining K+ homeostasis under salt stress conditions.