Abstract: In order to screen stable reference genes in cigar tobacco (BESNO H382) for quantitative real-time PCR (qRT-PCR), different tissues (such as roots, stalks and leaves at fast growing stage, sepals, corollas, stigmas, ovaries, stamens and pistils at full-bloom stage and seeds) of cigar tobacco cultured in greenhouse and leaves under different salt stresses (300 mmol/L NaCl treated for different durations) were used as study materials. Ten candidate reference genes screened from transcriptome data of cigar tobacco were analyzed by qRT-PCR, and the expression stabilities of those candidate genes were comprehensively evaluated by geNorm, NormFinder and BestKeeper. The results showed that RPL14A and UBC27 were the best reference genes for the different organs of cigar tobacco, and UBC28 was the best reference gene for cigar tobacco under the different salt stresses. Furthermore, the expression of stress related proline synthase gene P5CS under the salt stress was analyzed by using UBC27, UBC28 or RPL14A as a reference gene separately. The expression of P5CS was upregulated, and the expression levels of P5CS relative to the three reference genes were similar with comparable variation tendencies.