Mercury-resistant (Hg-R) bacteria occur in various bacterial species from a wide variety of environmental sources. Resistance is conferred by a set of operon genes termed the mer operon. Many Hg-R bacteria have been isolated from diverse environments and clinical samples, and it is recognized that mer operons are often localized on transposons. Previous research reports have suggested that Hg-R transposons participate in the horizontal gene transfer of mer operons among bacteria. This was confirmed by a study that found that mer operons were distributed worldwide in Bacilli with dissemination of TnMERI1-like transposons. In this mini review, possible strategies for transposon-mediated in situ molecular breeding (ISMoB) of Hg-R bacteria in their natural habitat are discussed. In ISMoB, the target microorganisms for breeding are indigenous bacteria that are not Hg-R but that are dominant and robust in their respective environments. Additionally, we propose a new concept of bioremediation technology for environmental mercury pollution by applying transposon-mediated ISMoB for environmental mercury pollution control.