Leptin gene (Lep) expression correlates with fat mass but differs between epididymal and inguinal fat depots in obesity. We investigated whether DNA methylation of a Lep enhancer (RS1) and the long non-coding RNA lncOb epigenetically regulate this depot-specific expression. We analyzed DNA methylation, Lep and lncOb expression in fat depots across metabolic states in male C57BL/6 mice using CRISPR-dCas9-KRAB-mediated repression, methylation-sensitive luciferase assays, and mass spectrometry. Under obesogenic conditions, RS1 methylation increased specifically in hypertrophic adipocytes of epididymal fat, repressing Lep transcription. This methylation persisted after long-term weight loss. LncOb expression correlated with Lep levels but was reduced in epididymal fat during obesity and remained suppressed post-weight loss. Together, our findings demonstrate that adipocyte Lep expression is dynamically regulated by depot-specific epigenetic mechanisms that become dysregulated in obesity and resist reversal by weight loss, providing a unifying molecular mechanism for depot-specific Lep expression differences in a state of obesity.