Plants respond to stress in part by modulating gene expression either constitutively or in an inducible manner which ultimately leads to the restoration of cellular homeostasis, detoxification of toxins, and recovery of growth. Upon introduction to various elicitors such as pathogen-associated molecular patterns, a massive reprogramming of plant gene expression is initiated. Differential display PCR offers rapid and multiple comparisons of gene expression to various stress durations and intensities. Nigella sativa has acclaimed many medicinal properties in traditional medicine. To explore the underlying molecular mechanisms in response to stress in the plants, Fusarium solani (a fungus) stress was induced at different time intervals ranging from 0 to 48 h. RNA was subjected to complementary DNA (cDNA) synthesis followed by PCR using different sets of anchored primers and arbitrary primers. The expression was visualized after silver staining on urea-PAGE. Out of the 23 upregulated re-amplified cDNA products, ten differential fragments showed significant homologies with domains related to cellular metabolism, signal transduction, and disease resistance. Such genes could be an informative source for developing genetically improved breeds under infectious stress.