The presented paper gives an insight into the genetic background of molecular diversity at the DNA level. Its potential sources, classified into two main categories depending on whether they lead to DNA sequence alternations (point mutations, insertions, deletions, chromosomal rearrangements, mobile elements etc) or changes in DNA methylation pattern, are discussed in parallel to their ?molecular markers? possible occurrence in the genome. A general overview of the most important sequences responsible for genetic variability (micro-, mini-, midi- and macrosatellites; transposones and retrotransposones) is given. Special attention is paid to different types of molecular marker systems and their most important applications. Molecular techniques are divided into several groups depending on the enzymes they use (endonucleases, T4 DNA ligase, Taq DNA polymerase or their combinations). Finally, investigation carried out with molecular markers in somaclonal embriogenesis is discussed.