Transposable elements are an important element of the complex genomic ecosystem. Transposable element insertion also appears to be bursty – either due to invasion of new transposable elements that are not yet repressed, de-repression due to instability of organismal defense systems, stress, or genetic variation in hosts. Here, we characterize the transposable element landscape in an important model Drosophila, D. serrata, and investigate variation in transposable element copy number between genotypes and in the population at large.  We find that a subset of transposable elements are clearly related to elements annotated in D. melanogaster and D. simulans, suggesting they spread between species more recently than other transposable elements. We also find that some transposable elements proliferate in particular genotypes compared to population levels. In natural populations an active transposable element and a potentially permissive background would not be held in association as in inbred lines, thus this could be a product of inbreeding. Yet many of the inbred lines have actively proliferating transposable elements suggesting that active transposable elements are not uncommon and that genotypes vary in their permissiveness in populations.