Prokaryote, viruses, and eukaryotes chromosomes contain fragments of DNA that can move and migrate to other parts of the chromosome. This movement is called Transposition and plays an important role in new combination of gene structure. DNA fragments that carry the genes or transposons are the transposable elements and may also called gene mutant agents. Transposons can move to another position of the same chromosome or other chromosomes. Genomic transposable elements are used in Mycology and Plant Pathology in various aspects, including the Cloning of genes effective in pathogenesis (Transposon tagging), or to identify specific races of virulent bacteria, viruses, and fungi in infected plant tissue, study of the evolutionary relationships of fungi, study of population structure and dynamics and epidemiology of fungal pathogenic isolates, in diagnosis of divergent populations and the introduction of transposon-based markers.