Detection of retrotransposons capable of contemporary transposition is hampered by the replicative nature of their movement and is usually limited to fortuitous observations of new integration events causing visible phenotypes. To circumvent this shortcoming, we developed a screening strategy for novel active retrotransposons containing long terminal repeats (LTR-TEs). Our approach is based on specific recovery of an LTR region that is part of the linear extrachromosomal DNA (ecDNA) synthetized in the reverse transcription step of the LTR-TE replication/transposition cycle. The method is inexpensive and straightforward and does not require prior knowledge of the retroelement sequence. Here we demonstrate the high sensitivity and specificity of this approach using Arabidopsis mutants with known retrotransposon activities. Using this method, we then identified a novel and mobile retroelement in the Landsberg erecta Arabidopsis ecotype that is absent in the annotated reference genome of Col-0. The cost-effective procedure presented here can be used to identify transposition-competent LTR-retrotransposons in a broad variety of biological specimens, independent of their sequence annotation.