Genetic variation may play a major role in how plants respond to activators of systemic acquired resistance. To examine this, the defence activator benzo(1,2,3)thiadiazole‐7‐carbothioic acid S‐methyl ester (BTH) was applied to seed of different breeding lines of tomato (Solanum lycopersicum) with diverse pedigrees, and the levels of induced resistance against Pseudomonas syringae pv. tomato, changes in defence gene expression and detrimental effects on seed germination and seedling emergence were measured. Two breeding lines, 7007 and 7024, were selected as non‐responsive and responsive to BTH. The SAR‐associated genes, SlPR1a and SlPR3b, were induced earlier or more strongly over the control prior to inoculation for line 7024 but not for line 7007. This was not observed for the ISR‐related genes, SlPin2 and SlPR2b. BTH inhibition of seed germination and seedling emergence was more delayed in line 7024 than 7007. However, applying BTH as a seed or soil drip reduced the delay. Thus, greater levels of BTH response have both positive (i.e., induced resistance and expression of SAR‐related gene expression) and negative (i.e., inhibition of seed germination and seedling emergence) effects and can differ significantly between genotypes. Thus, recommendations for use of induced resistance activators should include plant genotype recommendations and consider possible negative impacts of greater responsiveness.