Whirly is a kind of plant specific transcription factor which can combine with single strand DNA molecules, and plays a wide and complex role in the nucleus and organelles.To understand the function and evolutionary relationship of eggplant Whirly genes, bioinformatic analysis were performed to identify and characterize Whirly genes in eggplant genome, including the evolutionary relationship, gene structure, conservative motifs, cis acting elements in promoters. The expression mode of the genes wasalso analyzed in different tissues and under the treatments of exogenous hormone, low temperature and pathogen. The results showed that there were two Whirly gene members in eggplant genome, named SmWHY1 and SmWHY2, which were closely related to the tomato Whirly genes. Their expression can be detected in various tissues. SmWHY1 showed higher expression level than SmWHY2 in leaves, while SmWHY2 showed higher expression level than SmWHY1 in other tissues. The expression of two genes could be induced by abscisic acid, methyl jasmonate, salicylic acid, low temperture and pathogen, and the responses varied by gene and/or by treatments .Above results indicated that SmWHY1 and SmWHY2 may played important roles in the regulation of growth, development, and response to stress.