The ubiquitous and at the same time the least understood components of every eukaryotic genome are repetitive DNA sequences. They are divided into two groups: satellite DNAs (satDNAs), composed of sequences repeated in tandem, and transposable elements (TEs), interspersed throughout the genome. Due to their ability to reorganize and change their copy number, repetitive DNAs are crucial builders of genome architecture and drivers of genome evolution. The “mobilome” (the entire set of TEs in a genome) contributes strongly to eukaryote genome plasticity through bursts of activity. The evolution of satDNAs is governed by several well-established principles: organization into heterochromatin-associated long arrays, the “library model”, and “concerted evolution”. The research interest encompassing all aspects of bivalve biology is fast-growing, especially genome-wide “omics” analyses (including satellitomics and repeatomics). In our previous research, repetitive sequences of oysters have shown new patterns and exceptions from the canonical concepts, providing valuable contributions to the repetitive DNA biology. In addition, satDNAs in these organisms were shown to be closely linked to TEs. Employing different experimental and bioinformatic approaches, this research intends to explore the role of TEs in organization, propagation and evolution of satDNAs across a set of oyster species. We will examine the extent of “concerted evolution” and compare it between standalone and TE-incorporated satDNA arrays, both within and between species. The difference in the heterochromatin amount and content will be explored, and active parts of oyster mobilomes identified and compared. The study's findings will significantly advance our knowledge of repetitive genomic landscapes and their influence on chromosome structure. Importantly, comparative repeatomics will provide insights into the evolutionary processes and relationships of repetitive sequences in related species.