Due of their basal position in the vertebrate phylogenetic tree, the study on Elasmobranch genetics and cytogenetics can provide interesting information on the evolution of all vertebrates. In recent years, different molecular approaches, among them the physical mapping of specific nucleotide sequences on chromosomes and the use of these genomic portions for the construction of phylogenetic trees, were used to study the relationships between the different taxonomic groups of cartilaginous fishes. Particularly in Torpediniformes these are even more controversial. In addition, the species have different karyological parameters, the diploid number varies from 28 to 86 elements, with different morphology of the karyotype. Our aim was to report all the molecular markers that were used to reconstruct the phylogenetic position of Torpediniformes respect to the other Batoidea and to discriminate between the various chromosome pairs in the endemic species in the Mediterranean Sea. The 5S and 18S ribosomal DNA, the HpaI and Alu SINE, the telomeric (TTAGGG)n and the spermatogenesis-related sequences have proved particularly useful. These last genomic segments were also useful to differentiate between the male and the female karyotypes. Moreover the torpedoes showed a particular genomic organization, especially Torpedo torpedo; in this species large quantities of highly repeated DNA and a characteristic distribution of heterochromatin, which is never centromeric, were observed. The pattern of hybridization of these markers confirmed that the genome of Torpediniformes and particularly that of T. torpedo is now more than ever, unique, such as to consider this species as a "model species" to study.