Fusarium oxysporum f. sp. niveum (FON) and southern root-knot nematode (RKN, Meloidogyne incognita) are devastating soil pathogens of cultivated watermelon in the southeastern United States. The role of controlled micronutrient feeding [iron (Fe), manganese (Mn) and zinc (Zn)] via hydroponics on genes related to systemic acquired resistance [SAR, salicylic acid (SA) pathway genes (PR1, PR5, NPR1) and jasmonic acid (JA) pathway genes (VSP, PDF and LOX)] in watermelon seedling was investigated. Micronutrients were fed to the plants at higher (3X) and lower levels (0.5X) of recommended dose (X= recommended dose) for 7-days and the expression levels of the above-mentioned SAR genes were evaluated. A sub-set of micronutrient-fed plants were later inoculated with either FON or RKN or both and were re-evaluated at 3 day post inoculation for above mentioned genes. Two independent trials were conducted with three replications per treatment. Our results showed that JA-pathway genes (VSP and LOX) were upregulated in plants that were fed with micronutrients for 7 days. However, expressions of other SAR-related genes were downregulated and significant differences among treatments was only observed in PR1 expression. Upon pathogen inoculation, expression levels of JA and SA genes varied considerably for different micronutrient treatments. These observations indicate that micronutrient feeding in watermelon for 7-days can induce SAR genes and expression of JA or SA pathway genes can potentially be affected when either FON or RKN or both are present, irrespective of nutrient feeding.