An analysis of the evolution of the genus Nicotiana was carried out with physiological and molecular tools. The capacity of explants from seedlings of several species of Nicotiana to differentiate roots or shoots or to habituate was used to ascertain whether the in vitro behavior of species has a nonrandom distribution in the genus. The results obtained allowed us to identify two groups of species, one root-forming prone composed of Paniculatae (subgenus Rustica) and the other composed of Alatae, Repandae, and Noctiflorae (subgenus Petunioides), with a major tendency toward the production of shoots. Habituation capacity was characteristic of species randomly distributed throughout the phylogenetic tree. These data suggest fixation throughout the evolution of coadapted gene complexes (hormone-related genes) involved in the control of developmental processes. RAPDs, on the other hand, used as molecular markers for the clustering of related species, seem entirely coherent both with classical morphological and karyological studies and with in vitro physiological methods, supporting an early subdivision of the whole genus into two diverging developmental patterns.