The ability to generate genetic variation facilitates rapid adaptation in stressful environments. The opportunistic fungal pathogen
Candida albicans
frequently undergoes large-scale genomic changes, including aneuploidy and loss-of heterozygosity (LOH), following exposure to host environments. However, the specific host factors inducing
C. albicans
genome instability remain largely unknown. Here, we leveraged the genetic tractability of nematode hosts to investigate whether innate immune components, including antimicrobial peptides (AMPs) and reactive oxygen species (ROS), induced host-associated
C. albicans
genome instability.
C. albicans
associated with immunocompetent hosts carried multiple large-scale genomic changes including LOH, whole chromosome, and segmental aneuploidies. In contrast,
C. albicans
associated with immunocompromised hosts deficient in AMPs or ROS production had reduced LOH frequencies and fewer, if any, additional genomic changes. To evaluate if extensive host-induced genomic changes had long-term consequences for
C. albicans
adaptation, we experimentally evolved
C. albicans
in either immunocompetent or immunocompromised hosts and selected for increased virulence.
C. albicans
evolved in immunocompetent hosts rapidly increased virulence, but not in immunocompromised hosts. Taken together, this work suggests that host-produced ROS and AMPs induces genotypic plasticity in
C. albicans
which facilitates rapid evolution.