Abstract: To investigate the difference of multiple organic acid contents in tobacco of different genotypes under two ecological conditions, the multiple organic acid contents in flue-cured tobacco of 52 genotypes from Zhucheng in Shandong and Xichang in Sichuan were determined by gas chromatography. The results showed that malic acid, oxalic acid and citric acid were the major multiple organic acids, especially malic acid which accounted for about 75% of the total amount of multiple organic acids. There were 17 fluecured tobacco varieties whose multiple organic acid contents were higher than the average, most of which were foreign varieties. Most of the 18 flue-cured tobacco varieties with multiple organic acid content lower than the average were internal varieties. The multiple organic acid contents of 35 flue-cured tobacco varieties had good genetic stability. Overall, the absolute contents of multiple organic acids from Sichuan were low and relative contents were high. In particular, the absolute contents of malonic acid, citric acid were low and the relative contents of oxalic acid, malic acid, succinic acid were high for all the tested varieties. Shandong was the opposite of Sichuan. Both genotype and ecological condition significantly affected the multiple organic acid contents in flue-cured tobacco, but the effect of genotype was relatively higher.