Results are reported on the integration sites and copy number of alien marker genes neomycin phosphotransferase II (nptII) and β-glucuronidase (uidA), introduced into diploid potato Solanum tuberosum through transformation by Agrobacterium tumefaciens. Also, the transgenic potato chromosomes 3 and 5 harbouring the nptII and uidA genes, which were transferred to tomato (wild species Lycopersicon peruvianum) by microprotoplast fusion, as revealed by genomic in situ hybridization (GISH), were identified by RFLP analysis using chromosome-specific markers. The data revealed three integration sites in the donor potato genome, each containing the uidA gene, and two also harbouring the nptII gene. Analysis of monosomic-addition hybrid plants obtained after microprotoplast fusion showed that each of these three integration sites is located on a different potato chromosome. The microprotoplast hybrid plants contained only the chromosomes that carried the selectable gene nptII. The data on sexual transmission of the donor potato chromosome carrying the uidA and nptII genes were obtained by analyzing the first backcross progeny (BC1) derived from crossing a monosomic-addition hybrid plant to tomato (L. peruvianum). The glucuronidase (GUS) assay and PCR analysis using primers for the uidA gent indicated the presence of the potato chromosome in GUS-positive and its absence in GUS-negative BC1 plants. RFLP analysis confirmed sexual transmission of the potato chromosome carrying the nptII and uidA genes to the BC1 plants. A few BC1 plants contained the nptII and uidA genes in the absence of the potato additional chromosome, indicating that the marker genes were integrated into the tomato genome. The potential applications of the transfer of alien chromosomes and genes by microprotoplast fusion technique are discussed.