Long-noncoding RNA AC092159.2, located similar to 247 bp upstream of the TMEM18 gene, may play integral roles in metabolic processes, including adipocyte differentiation and glycometabolism. AC092159.2 may be an important regulator of TMEM18, which is an important susceptibility gene related to obesity and type 2 diabetes. We designed a case-control study (including 964 gestational diabetes mellitus [GDM] cases and 1021 controls) to assess the associations of 14 single-nucleotide polymorphisms (SNPs) in AC092159.2 with the GDM risk. Logistic regression analyses showed that rs11127496 A > G, rs12714417 C > T, and rs1320334 A > G conferred a decreased GDM risk in the recessive and additive model, whereas rs11691220 T > C conferred an increased GDM risk in the dominant and additive model. Also, with increasing number of protective alleles of the four SNPs, the risk of GDM was significantly decreased in a dose-dependent manner (p(trend) = 0.007). Further function annotation indicated that these four SNPs may fall on the function elements of human pancreatic islets. The genotype-phenotype associations suggested that these SNPs may contribute to GDM by affecting TMEM18 expression. AC092159.2 SNPs (rs11127496 A > G, rs11691220 T > C, rs12714417 C > T, and rs1320334 A > G) may be susceptibility makers for risk of GDM in Chinese females.