Potato common scab is a worldwide disease characterized by the presence of corky lesions on tubers. This disease is caused by the soil-borne pathogenic actinobacterium Streptomyces scabiei which synthesizes the phytotoxin thaxtomin A (TA) that is essential for the infection of tubers. Our laboratory has developed a technique to increase resistance to common scab using habituation to TA in the variety Russet Burbank. The TA-habituated somaclone called RB9 was significantly more resistant to common scab compared to the parent variety (RB). Proteomics analyses of RB9 tubers compared to RB tubers showed an increased abundance in proteins associated with defense and storage, particularly, lipoxygenases (LOX). These enzymes are involved in the metabolism of fatty acids and the synthesis of signaling and defense compounds. TA habituation in the Kennebec variety also led to the production of somaclones with increased resistance to common scab. As found for RB9, the Kennebec somaclone K-39 showed an increase in the abundance of LOX compared to the original variety, suggesting that LOX may be involved in the defense against S. scabiei. This was supported by the observation that S. scabiei infection also induced LOX accumulation in minitubers. To assess the role of LOX in the protection against common scab, minitubers developing on RB and RB9 leaf buds were treated with jasmonic acid, salicylic acid and naproxen to increase or reduce LOX abundance during S. scabiei infection. Our results suggest that reduction in LOX levels promotes S. scabiei infection.