We identified 272 DMPs that were differently methylated between GDM and non-GDM across two time points during pregnancy, and several genes that could be involved in the pathophysiology of GDM such as SELP, LGR6, NBL1, RPS6KA2 or ADCYAP1R1. We also detected three DMPs, cg01459453, cg15329406, and cg04095097, that adequately discriminated GDM occurrence and replicated one of these in an independent cohort. Here, RPS6KA2 is linked to gestational diabetes.