Candida albicansis a frequent colonizer of human mucosal surfaces as well as an opportunistic pathogen.C.albicansis remarkably versatile in its ability to colonize diverse host sites with differences in oxygen and nutrient availability, pH, immune responses, and resident microbes, among other cues. It is unclear how the genetic background of a commensal colonizing population can influence the shift to pathogenicity. Therefore, we examined 910 commensal isolates from 35 healthy donors to identify host niche-specific adaptations. We demonstrate that healthy people are reservoirs for genotypically and phenotypically diverseC.albicansstrains. Using limited diversity exploitation, we identified a single nucleotide change in the uncharacterizedZMS1transcription factor that was sufficient to drive hyper invasion into agar. We found that SC5314 was significantly different from the majority of both commensal and bloodstream isolates in its ability to induce host cell death. However, our commensal strains retained the capacity to cause disease in theGalleriamodel of systemic infection, including outcompeting the SC5314 reference strain during systemic competition assays. This study provides a global view of commensal strain variation and within-host strain diversity ofC.albicansand suggests that selection for commensalism in humans does not result in a fitness cost for invasive disease.