Seven wild type strains of D. melanogaster and D. simulans were assayed for the typical histone post translational modifications described above and RNA steady state level. We observed variable histone patterns between both species and wild type strains, and between different TE families. We also observed RNA transcript variation among strains and species. The complex pattern that we observed with no fixed associations between histone marks and TEs suggest that the activity of TEs may be uncoupled with the histone marks, and that a few specific copies of TEs may be responsible for most of the observed TE activity. Several studies have suggested that the epigenetic regulatory system might be flexible. The epigenetic polymorphism observed between twin brothers and the presence of different gene methylation patterns in different Arabidopsis thaliana ecotypes exemplify natural epigenetic variation. In addition, large differences in TE copy numbers are often observed between closely-related species. These observations suggest that, although in most circumstances TEs are efficiently silenced, the balance between TE activity and silencing can be altered in the wild. In order to understand TE dynamics, it therefore appears essential to integrate epigenetic and natural population analyses, as many authors have recently pointed out. Nevertheless, the study of variation in natural populations harbors intrinsic difficulties due to variation in genetic background, environment, global and single effects on expression etc. Here, we have attempted to shed light on the epigenetic variation that may exist within transposable elements of different wild type strains. We have demonstrated that TE families possess different chromatin states, such as the roo element, which is the only TE in our analysis constantly devoid of constitutive repressive marks. Roo is highly expressed and abundant in both D. melanogaster and D. simulans species. Hence, roo is the only TE family to present a clear histone and expression profile, and is the only profile common to both species. We have confirmed the recent findings that the pattern of histone modifications associated with Drosophila TEs is more complex than in other species. We have also shown that two close species, D. melanogaster and D. simulans, harbor FG-4592 distinct patterns of TE expression and chromatin state. For all TEs analyzed, D. melanogaster has an average higher copy number and expression but TEs are also highly associated with repressive histone marks. Interestingly, the expression of writers of such heterochromatic marks, Su3–9 and E, is nearly absent in D. simulans wild type strains, where TEs are less abundant than in D. melanogaster. The biological meaning of this disparity remains unknown. Finally, we found no significant correlation between the expression, chromatin state or copy number of TEs in wild type strains of D. simulans. We have previously shown that different copies of the same TE family can harbor distinct histone posttranslational modifications. Therefore, it is extremely plausible that the data discussed here is a reflection of the majority of the copies found in the genome, but in no way a detailed description of the epigenetic marks that TE copies may harbor in Drosophila. The master copy hypothesis postulates that only one active copy is necessary to maintain retrotransposition. Nevertheless, very often, more than one full length copy is observed in the genomes and truncated copies that do not retrotranspose are still able to produce transcripts. Therefore, the complete transcriptome of a transposable element is complex and hard to understand.