Background: Transposable elements (TEs) are major players in evolution. We know that they play an essential role in genome size determination, but we still have an incomplete understanding of the processes involved in their amplification and elimination from genomes and populations. Taking advantage of differences in the amount and distribution of the Long Interspersed Nuclear Element ( LINE), helena in Drosophila melanogaster and D. simulans, we analyzed the DNA sequences of copies of this element in samples of various natural populations of these two species. Results: In situ hybridization experiments revealed that helena is absent from the chromosome arms of D. melanogaster, while it is present in the chromosome arms of D. simulans, which is an unusual feature for a TE in these species. Molecular analyses showed that the helena sequences detected in D. melanogaster were all deleted copies, which diverged from the canonical element. Natural populations of D. simulans have several copies, a few of them full-length, but most of them internally deleted. Conclusion: Overall, our data suggest that a mechanism that induces internal deletions in the helena sequences is active in the D. simulans genome.