Background: Candida species have long been recognised as aetiological agents of opportunistic infections of the oral mucosa, and more recently, as players of polymicrobial interactions driving caries, periodontitis and oral carcinogenesis. Methods: We studied the clonal structure of Candida spp. at oral niche resolution in patients (n = 20) with a range of oral health profiles over 22 months. Colonies from oral micro-environments were examined with multilocus sequencing typing. Results: Candida spp. identified were C. albicans, C. glabrata and C. dubliniensis. Increased propensity for micro-variations giving rise to multiple diploid strain types (DST), as a result of loss of heterozygosity, was observed among C. albicans clade 1 isolates compared to other clades. Micro-variations among isolates were also observed in C. dubliniensis contra to expectations of stable population structures for this species. Multiple sequence types were retrieved from patients without clinical evidence of oral candidosis, while single sequence types were isolated from oral candidosis patients. Conclusion: This is the first study to describe the clonal population structure, persistence and stability of Candida spp. at oral niche level. Future research investigating links between Candida spp. clonality and oral disease should recognise the propensity to micro-variations amongst oral niches in C. albicans and C. dubliniensis identified here.