Zbtb16-encoded PLZF is a signature transcription factor (TF) that directs the acquisition of T helper effector programs during the development of multiple innate lymphocyte lineages, including NKT, ILC, MAIT and gammadelta ineages. It is also essential in osteoblast and spermatogonial development. How Zbtb16 itself is regulated in different lineages is incompletely understood. By systematic Crispr/Cas9-assisted deletions of chromatin accessible regions within the Zbtb16 locus in mouse, we identified a dominant critical enhancer controlling PLZF expression exclusively in innate lymphoid lineages, including ILC,  and NKT,  MAIT and gammadelta lineages precursors. Multiple sites within this enhancer expressed canonical motifs for the TF Runx1, which was essential for the development of both ILC and NKT lineages. Notably, some of these regulatory sites exerted an impact on NKT cell development by controlling the kinetic rather than the overall level of PLZF expression. Thus, a comprehensive unbiased analysis of regulatory elements in vivo revealed critical new mechanisms of PLZF regulation shared between innate and innate-like lymphoid lineages.