Retrotransposon-like elements are a principal componment of most eukaryotic gnomes,representing roughly 90% of wheat (Triticum aestivum) genomes.According to our unpublished previous studies on AFLP(Amplified Fragment Length Polymorphism),a retrotransposons is considered as a mutation factor about the Low Energy ion Beam implanting on wheat.the reverse transcriptase (RT) domain of Ty1-copia-like Retrotransposons in wheat(including treated with ion beam and untreated) were obtained by Reverse-transcriptional Polymerase Chain Reaction(RT-PCR) and cloned one hundred approximately clones were obtained,42 clones are from the untreated group(CK),65 clones are from the treated group with ion beam(CL).Sequence analysis of each clones is done by the softwares.Phylogeny and classification are computed responding to the RT domain.All the results showed that there is a much diversity on RT domain between the untreated group and the treated with ion beam group,especially,the retrotransopons of the treated group had more intact and functional clones,less defective,than the retrotransopons of untreated group.It suggested that retrotransposons of two groups impact on the host gene expression in two different way and had different functions in cell and low energy can influence the expression of the retrotransposons in wheat.