Transposable elements (TEs), acting as symbiotic entities within host genomes, their landscapes represent a pivotal subject in evolutionary discourse. Previous investigations on the impact of ecological niches on the shaping of TE landscapes have yielded inconsistent conclusions. This study assessed the effect of ecological niches on the dynamics of TEs, employing pollinating fig wasps and non-pollinating fig wasps (NPFWs) residing in the syconia of figs as models. Our findings reveal a significantly positive correlation between TE content and genome size, exhibiting conspicuous phylogenetic signal. Significant differences emerge in the quantity, total length, and family types of TEs between pollinators and NPFWs. Notably, pollinators exhibit ‘dormant’ TE landscapes characterized by inactivity along with rapid decay attributable to smaller effective population sizes. This results in only a few remnants persisting over nearly a million years. Despite the relaxed selection pressure on pollinators in an effort to prolonging TE retention, their abundance remains limited. In contrast, NPFWs exhibit ‘aggressive’ TE landscapes, marked by the continual generation of new insertions. The larger effective population sizes contribute to decelerating the decay of TEs, as demonstrated by the substantial TE accumulation in the last one million years. These observed dynamics are intrinsically linked to the distinctive ecological niche provided by figs. TE remains suggest a functional role in facilitating pollinators’ adaptation to stress induced by their niche. Numerous cis-regulatory modules that originate from TEs and locate near genes involved in processing environmental information, which emphasizes their potential functional significances.