Candida species are considered the primary causative agents of denture stomatitis, but their role in colonization and disease in denture wearers remains undefined. In this study, we investigated risk factors associated with progression to Candida-related denture stomatitis in patients using complete dentures, and we genetically identified Candida isolates associated with disease and colonization. We recruited 114 retirement home residents for this study, from whom oral mucosa samples were collected and cultured following oral cavity exams. Morphologic analysis was used to identify potential yeast-positive cultures, which were then characterized further by RFLP analysis. C. albicans was the most frequently recovered species (61; 41.5%), followed by C. glabrata (27; 18.4%), and C. tropicalis (19; 12.9%). In addition, 16 isolates (10.9%) of C. dubliniensis were recovered, which was the first identification of this species in clinical samples from Iran. This study demonstrated a significant association between the duration of denture wear and oral candidiasis. Furthermore, we noted a high prevalence of C. dubliniensis in complete denture wearers.