Transposable elements (TEs) represent a major component of diverse genomes, can generate large-effect mutations,affect adaptive evolution. Despite their significant role in various evolutionary processes, the regulatory mechanisms governing TE abundance variation remain an enigma. This review synthesizes current knowledge about the evolutionary dynamics of TEs in natural populations of Arabidopsis, emphasizing forces driving TE abundance variation. In addition, we pay more attention to the influence of epigenetic factorsenvironmental stresses on TE activityhighlight the genetic architecture of TE transposition in natural populations. Finally, we review the progress in characterization, identification,applications of active TEs, which are among the major contributors to TE abundance,suggest directions for future study. Overall, we aim to resolve the enigma of TE abundance by outlining its potential drivers.