The methylation status of eight individual CpG sites were identified as differing significantly between GDM and control groups by qualitative analysis, and these were located in the promoter regions of RDH 12, HAPLN3, NFATC4, YAP1, and DNAJB6, and the intron region of C5orf34. Importantly, we found that the methylation statuses of four CpG sites were significantly associated with GDM occurrence, namely CpG site 89438648 (HAPLN3), 68167324 (RDH12), 157130156 (DNAJB6), and 24837915 (NFATC4), using conditional logistic regression analysis. This evidence concerns the gene DNAJB6 and gestational diabetes.