In tomato, the stolbur disease caused by ‘Candidatus Phytoplasma solani’ alters developmental processes resulting in malformations of both vegetative and reproductive organs, two stolbur phytoplasma strains PO and C induce mutually distinct symptoms. The aim of the present study was to determine the effect of stolbur phytoplasma-infection on the Salicylic (SA) and Jasmonic (JA) acids hormone signalling pathways and to assess whether pre-activation of these defence pathways could protect tomato against the stolbur disease development. Expression of SA- and JA-dependent marker genes was studied in tomato by qRT-PCR. Results indicated that the SA-mediated defence response was activated by the stolbur phytoplasma strains PO and C in contrast to the JA-dependent defence pathway which was repressed by strain PO but activated by strain C. The two stolbur strains, PO and C, generated different responses, suggesting that the two strains might have distinct virulence factors, in agreement with the fact that they induce distinctive symptoms. In stolbur PO-infected tomato, pre-activation of the JA-dependent defence pathway by methyl jasmonate (MeJA) before infection had no effect on the disease development whereas pre-activation of the SA-dependent defence pathway by treatment with benzothiadiazole (BTH) prior to graft-inoculation of the phytoplasma resulted in a minor delay in phytoplasma multiplication and symptom production. As grafting implicates a high inoculum as compared to insect inoculation, it would be of interest to test BTH treatment in natural conditions.