Gut microbiota can have a distant effect on immune function in the lung through the gut–lung axis. This study observed that the specific expansion of the commensal fungus Wallemia mellicola in the gut (that is, without overgrowth of the total fungal community in the gut) enhances the severity of allergic airway disease in mice. Whereas mice with a healthy gut microbiota were able to resist a population expansion when gavaged with live spores of W. mellicola, mice that had been treated with antibiotics did not. Mice that had increased levels of W. melliola in the gut experienced alterations in a number of pulmonary immune responses to inhalation of the house dust mite antigen (an aeroallergen). Colonization of fungus-free altered Schaedler Flora mice with W. mellicola enhanced the severity of allergic airways disease, suggesting that any changes in bacterial community composition do not have a role in this phenomenon.