Henan and Guizhou are two major flue-cured tobacco growing areas in China, with distinct climatic conditions. Higher characteristic temperatures and longer sunlight periods in Henan and relatively low temperatures and shorter sunlight periods in Guizhou during the maturing stage of flue-cured tobacco. Flue-cured tobacco from Henan typically has a stronger aroma and it is more irritant compared to the tobacco from Guizhou. To elucidate the molecular changes in the tobacco grown in the two different areas, leaf samples were collected at the mature stage and gene expression involved in the carbon and nitrogen metabolism pathway were examined using PCR methods. Seven genes which included ZDS (Zeta-carotene desaturase), CHL (Chlorophyllase), GS1-3 (Glutamine synthetase), Nir-3 (Ntrite reductase 3), Hex (Hexokinase), SPP2 (Sucrose-6-phosphate phosphatase) and TPP (Trehalose-phosphate phosphatise) were identified as differently expressed between two cultivars and all of them expressed at higher level in Jiucanping 2 compared with that in Bina 1. Compared with the plants grown under Baofeng environment both Nir-3 gene in Bina1 and Hex gene in Jiucaiping 2 expressed at a lower level as well as CSlE (Cellulose synthase-like protein) gene expressed at a higher level in both cultivars. Results showed that some pivotal genes expressed at lower level in Bina 1 indicating that physiological activities in the corresponding metabolism pathway were much weaker compared with that in Jiucanping 2. The nitrogen metabolism pathway in Bina 1 and sugar metabolism pathway in Jiucaiping 2 were affected mostly by environment. Results also indicated that higher temperature was conducive to nitrogen metabolism.