Transposable elements (TEs) are DNA sequences capable of mobilization from one genome location to another. Since the discovery of ‘Dissociation (Dc) locus’ by Barbara McClintock in maize (1), mounting evidence in the era of genomics indicates that a significant fraction of eukaryotic genomes is composed of TE sequences, involved in various aspects of biological processes such as development, physiology, diseases, and evolution. Although technological advances in genomics have discovered numerous functional impacts of TE across species, our understanding of the TEs is still an ongoing process due to challenges resulting from the complexity and abundance of TEs in the genome. In this mini-review, we briefly summarize the biology of TEs and their impacts on the host genome, emphasizing the importance of understanding TE landscape in the genome. Then, we introduce the recent efforts, especially in vivo retrotransposition assays and long read sequencing technology for identifying de novo insertions/TE polymorphism, which will broaden our knowledge of the extraordinary relationship between genomic cohabitants and their host.