Nicotiana tabacumis a plant containing cellular T-DNA (T-DNA obtained by plants fromAgrobacteriumduring evolution as a result of horizontal gene transfer) in the genome. Within the speciesN. tabacum, many varieties are distinguished, and phylogenetic relationships among them have not been established yet. Despite the diversity of phenotypes,N. tabacumvarieties are known to have a low level of genetic diversity, so clarification of intraspecific phylogeny is complicated. This article proposes a new marker for studying the phylogeny of theNicotiana tabacumspecies on the basis of the results of a comparative analysis of the cT-DNA TA and TB fragments and thePMT2gene in 11 varieties ofNicotiana tabacum. It has been shown that, for sequences of agrobacterial origin in the genomes of plants, the same evolutionary mechanisms are typical, as for plant sequences. Thus, the cT-DNA (namely, TA) sequences can be used as a phylogenetic marker for the speciesN. tabacum, since the varieties can be separated into two groups based on the structure of the TA central region.