Transposable elements (TEs) are DNA sequences able to change position in the genome, and represent more than 40% of mammalian genetic material. TEs can have positive or detrimental effects on the host, being both important motors of evolution and genomic threats, and are associated with diseases such as cancer and diabetes. Growing evidence indicates the host co-opts TEs for its benefit, with examples such as syncytins – genes important for placental formation that derive from TEs. Given their potential damaging role, the host needs to repress TEs, especially during early embryogenesis. KRAB-containing zinc finger proteins (KRAB-ZFPs) are important regulators of TEs, which they repress with their cofactor KAP1. In stem cells, the KRAB/KAP1 complex irreversibly silence TEs and is believed to be dispensable in adult cells. KRAB-ZFPs constitute one of the largest families of transcriptional regulators encoded by higher vertebrates, but functional information is missing for most of its members. To shed light on this important family of transcription factors, we first developed a large-scale functional screen matching murine TEs with their cognate KRAB-ZFP. The screen identified KRAB-ZFP809 as the ligand of its previously mapped DNA target in the murine leukemia virus genome. Our method further singled out two novel KRAB-ZFPs binding to TE sequences, as confirmed by repression and binding assays. One of them, Gm6871, was identified to regulate LINE-1 elements together with KAP1 in embryonic stem cells. KAP1 regulation followed a chronologically conditioned pattern, repressing elements that entered the mouse genome between 5.6 and 3.8 million years ago, suggestive of an evolutionary arms race between host KRAB-ZFPs and TEs. Secondly, we found the paralogs ZFP932 and Gm15446 to bind overlapping but distinguishable subsets of ERVK (endogenous retrovirus K), to repress these elements in embryonic stem cells, and to regulate secondarily the expression of neighboring genes. Furthermore, we uncovered that these KRAB-ZFPs and KAP1 control TEs in adult tissues, in cell culture and in vivo, where they partner up to modulate cellular genes. Our results establish an efficient screening method to identify KRAB-ZFPs DNA targets, opening the way to functional analyses of this major class of transcriptional repressors. Most importantly, our study strongly suggests that KRAB-ZFP genes are not only part of an evolutionary arms race with TEs, but also participate in the domestication of these elements for the benefit of the host. Given the abundance and high degree of species-specificity of TEs and KRAB-ZFPs, these results have important implications for understanding the biology of higher vertebrates, including humans.