Phylloplane microbes have been studied as strategic tools in management against plant pathogens. Non-pathogenic bacteria and fungi have been applied as crop protectants against various plant diseases. The present study aimed at evaluating the potentiality of Aspergillus niger spores in altering the activity of four key enzymes related to defense in tomato. The experiment was designed such that two groups of 50 tomato plants were considered: group 1 – sprayed with autoclaved distilled water (control) and group 2 – sprayed with A. niger spores. Spraying was carried out under aseptic conditions. The experimental parameters included analysis of the activity of peroxidase (POX), polyphenol oxidase (PPO), phenylalanine ammonia lyase (PAL) and tyrosine ammonia lyase (TAL) as well as expression of POX and PPO isoforms. The results demonstrated an inductive effect of A. niger on the activity of POX, PPO, PAL and TAL. Enhanced expression of POX and PPO isoforms was also observed. The results indicated that A. niger can be considered probiotic for the management of tomato against its phytopathogens.