Transposable elements (TEs) can represent major sources of genomic variation across eukaryotes, providing novel raw material for species diversification and evolutionary innovation. While considerable effort has been made to study their evolutionary dynamics across vertebrates, arthropods, and plants, bivalves represent a substantially understudied group, with few comparative studies in literature. As a consequence, their role in shaping bivalve genome evolution is largely unknown although TEs have been hypothesized to be involved in the evolution of multiple genomic oddities, such as high levels of gene presence-absence variation high levels of hemizigosity and a horizontally transmissible leukemia-like disease. The family Ostreidae (order Ostreida), whose diversification started ~250 Mya is one of the most studied bivalve groups because of their economic importance and invasiveness of some species (e.g. the Pacific Oyster Crassostrea gigas). This order includes the bivalves with the smallest genomes in terms of both genome size and chromosome number, but are characterized by a relatively high repetitive content. Moreover, DNA and Rolling Circle transposons hosted by C. gigas seem to have been highly active in recent years, contributing to up to 80% of the total structural variants (SVs). However, nothing is known about their nature and their possible impact in genome evolutionary dynamics. Recent advances in their genomic resources offer the first important opportunity to study genome size, transposable element evolution and their impact on overall genome stability also in this emerging model system.