Gut mycobiota dysbiosis can negatively impact the outcome of several diseases of inflammatory origin, suggesting a role of the mycobiota in influencing the host immunity. However, it is unknown whether the gut mycobiota composition can create an immune environment that would influence the immune response to a newly introduced intestinal fungus. Using ITS1 deep sequencing, we evaluated the mycobiome structure of C57BL/6J mice acquired from Jackson (JAX) or bred in a controlled environment at a dedicated room in our own mouse facility (WCM-CE) for several generations. We found that C57BL/6J mice from these segregated mouse colonies harbor dramatically different mycobiota. To assess whether the mycobiota make up can influence immune responses to colonization with a fungus foreign to the murine GI tract, we colonized JAX and WCM-CE mice with the human commensal C. albicans and measured Th17 responses in the gut. We found that independent of mycobiota composition, mice produced strong Th17 responses to gastrointestinal C. albicans colonization. Our data suggest that different mouse colonies can carry dramatically different mycobiota. Nevertheless, strong Th17 responses to a newly introduced opportunistic commensal fungus are potently induced independent of the mycobiota background in this experimental setting.