Abiotic stress conditions caused by temperature extremes, water availability, and ion toxicity severely limit plant growth and productivity. The degree of damage depends on the duration and intensity of the stress, developmental stage and plant species. Plants respond to stress through changes in gene expression, which are controlled by multiple signaling pathways. Our research has focused on gene expression analysis during low temperatures in cold-hardy Poncirus trifoliata, used as rootstock for enhancing cold tolerance in Citrus unshiu (Satsuma mandarin) scion in freeze-prone crop production areas. cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) and Quantitative Real-Time (RT) PCR were use to compare expression patterns in rootstock and C. unshiu grafted onto P. trifoliata. Genes with the following known functions were identified: signal transduction and regulation of gene expression (such as MAPK3), osmotic stress response, cell skeleton organization, vesicle trafficking and senescence. Differential expression of genes in roots of drought tolerant cucurbit species (Citrullus colocythis) is being studied in response to drought and plant hormones. A complex interplay between abscisic acid, jasmonic acid and salicylic acid signaling pathways regulates gene expression during adaptive responses to abiotic stress in Citrullus species. Functional analysis and detailed characterization of abiotic stress related genes is in progress.