Within Solanaceae, Nolana L. f. and Sclerophylax Miers are two genera that have deserved special attention because of their rare anatomical characteristics. However, they are poorly known from the cytogenetic perspective. In order to discuss their chromosome features in an evolutionary context, classical staining, chromomycin A(3)/4-6-diamidino-2-phenylindole (CMA/DAPI) fluorescent banding and in situ hybridisation (FISH) with probes for the 18-5.8-26S and the 5S rDNA loci were applied to root tips of germinating seeds. All the species presented the chromosome number 2n=24. Karyotypes were highly symmetric, with most chromosomes being metacentric and with a maximum of three submetacentric pairs in N. divaricata. The CMA/DAPI banding technique, assayed for the first time in Sclerophylax, showed CMA(+)/DAPI(-) bands associated with nucleolar organiser regions (NORs) in the first metacentric chromosome pair in each species. The FISH technique (applied to four species of Sclerophylax and, for the first time, in one species of Nolana) showed that the 18-5.8-26S loci coincide with CMA(+)/DAPI(-) bands. Three Sclerophylax species presented two pairs of 5S signals, whereas S. adnatifolia showed three. The rDNA loci resulted as asyntenic in Sclerophylax, but were localised in the same chromosome in N. divaricata. Despite the morphological peculiarities of Nolana and Sclerophylax, the chromosome number and karyotype features are consistent with the position of the two genera within the x=12 clade', while the number and position of rDNA loci established the chromosome rearrangements, suggesting different evolutionary pathways with respect to their closest relatives, Lycium and Jaborosa.