The Mutator system of maize has been described as the most active and mutagenic plant transposon. The autonomous element MuDR contains two genes: mudrA encoding the transposase and mudrB whose product function remains undetermined. MudrA-like coding domain showed to be the most abundantly expressed transposon-related sequence in sugarcane transcriptome. A previous report identified the existence of at least four clades of mudrA-like sequences in sugarcane, rice and arabidopsis, which already existed prior to the Monocot-Eudicot split. To gain understanding about the abundance, distribution, copy number and diversity of mudrA-like sequences, a comparative study between sugarcane and rice was performed. As a result, it was possible to identify that copy number greatly differs and, at least in grasses, there was a class-specific amplification with a burst of Class II elements. Structural analyses performed on rice genomic sequences revealed that while Class I and Class II clades comprise elements with transposon features, Class III and Class IV no longer possess TIRs and correspond to domesticated transposases.