This study investigates the prevalence, drug resistance, and genetic diversity of Candida glabrata, a significant non-albicans Candida species, among pregnant women in Hainan, China. We collected 3,806 reproductive tract secretion samples from women with vaginal discomfort and isolated 594 Candida strains, including C. albicans (45.1%), C. glabrata (36.2%), C. dubliniensis (12.2%), C. parapsilosis (2.7%), C. tropicalis (2.7%), and C. krusei (1.2%). Antifungal susceptibility testing showed that 64.5% of the isolates were intermediate or resistant to at least one of four antifungal agents: fluconazole, itraconazole, voriconazole, and amphotericin B. Among 215 C. glabrata isolates, 81.4% were intermediate or resistant to at least one antifungal, with 10% showing resistance to multiple agents. Multilocus sequence typing (MLST) of 52 C. glabrata strains from the reproductive tract, 53 from oral cavities, and 17 from environmental sources revealed 14 sequence types (STs), with six STs shared among these niches, indicating a highly clonal population structure. Comparisons with the global MLST database showed both shared and distinct characteristics among C. glabrata populations in Hainan and other regions, highlighting significant differentiation. We discuss the implications of these findings to the epidemiology and evolution of this pathogen.