Significance Transposable elements (TEs) are genetic units that can selfishly propagate in a host genome. Despite often being considered “junk,” TEs can occasionally acquire useful functions such as regulating expression of nearby host genes. Here, we study gibbons, small apes whose genome contains a unique TE called LAVA (LINE- Alu Sz-VNTR- Alu _LIKE ). We present evidence indicating that several LAVA insertions function as gene regulatory elements in the gibbon genome. Two of these insertions were also favored/preserved by natural selection, further indicating their functional importance for gibbons. Both of these LAVA elements were found inside genes that facilitate correct repair of DNA breaks, suggesting that LAVA’s incorporation in these genes may have influenced the regulation of biological processes that are crucial for maintaining genome integrity.