Mutator-like transposable elements (MULEs) represent a unique superfamily of DNA transposons as they can capture host genes and cause higher frequency of mutations in some eukaryotes. Despite their essential roles in plant evolution and functional genomics, MULEs are not fully understood yet in many important crops including barley ( ). In this study, we analyzed the barley genome and identified a new mutator transposon . This transposon is present at extremely high copy number in barley and shows unusual structure as it contains three open reading frames (ORFs) including one ORF (ORF1) encoding mutator transposase protein and one ORF (ORFR) showing opposite transcriptional orientation. We identified homologous sequences of in both monocots and dicots and grouped them into a large mutator family named . transposons from different species share significant sequence identity, but they exhibit distinct sequence structures. Unlike the transposase proteins which are highly conserved between transposons from different organisms, the ORFR-encoded proteins are quite different from distant species. Phylogenetic analysis indicated that transposons shared closer evolutionary relationships with the maize transposon than other reported MULEs. We also found phylogenetic incongruence for the transposons identified in rice and its wild species implying the possibility of horizontal transfer of transposon. Further comparison indicated that over 200 barley genes contain -related sequences. We analyzed the barley pan genomes and detected polymorphic transposons between the sequenced 23 wild and cultivated barley genomes. Our efforts identified a novel mutator transposon and revealed its recent transposition activity, which may help to develop genetic tools for barley and other crops.