During two last decades, new regulations and consumers pressure encouraged the professionals of the tobacco to develop new varieties with the aim to enhanced safety for the consumer. Significant results were obtained by conventional means concerning some major chemical compounds of smoke tobacco. However, this evolution is relatively slow, and the use of new tools to evaluate genotypes such as molecular markers should offer the possibility to progress more quickly. Identification of principal genes implied in the formation of some precursors of polynuclear aromatic hydrocarbons and nitrosamines is in progress, and should make it possible to have more powerful means of assessment rapidly. Obtaining varieties of tobacco resistant to principal pathogens is important too because the use of pesticides is reduced significantly and a consequent number of molecular markers is now at the disposal of the breeder. Finally the achievement of a genetic map of tobacco should be essential in the future to identify genomic areas linked to complex characters such as tar yield of smoke.