Like ecological communities, which vary in species composition, eukaryote genomes differ in the amount and diversity of transposable elements (TEs) that they harbor. Given that TEs have a considerable impact on the biology of their host species, we need to better understand whether their dynamics reflects some form of organization or is primarily driven by stochastic processes. Here, we borrow ecological concepts on species diversity to explore how interactions between TEs can contribute to structure TE communities within their genomic ecosystem. Whereas the niche theory predicts a stable diversity of TEs because of their divergent characteristics, the neutral theory of biodiversity predicts the assembly of TE communities from stochastic processes acting at the level of the individual TE. Contrary to ecological communities, however, TE communities are shaped by selection at the level of their ecosystem (i.e. the host individual). Developing ecological models specific to the genome will thus be a prerequisite for modeling the dynamics of TEs.