human gastrointestinal (GI) tract is home to trillions of microorganisms, some beneficial and otherspotentially harmful. Recent advances in science have allowed us to identify the multitude of organismsinhabiting the GI tract and parse out those that play a role in inflammatory bowel disease (IBD). Unfortu-nately, most research has focused on studying only the bacteria while ,overlooking a key player, fungus.In order to address this issue, we have focused our efforts on studying the fungal community in the GItract known as the mycobiome. We found that patients with Crohn’s disease (CD) tend to have muchhigher levels of the fungus Candida tropicalis compared to their healthy family members, as well as twobacteria, Escherichia coli and Serratia marcescens. Furthermore, we showed that these three organismsworked together to form robust biofilms capable of exacerbating intestinal inflammation. Herein, wediscuss the role of the mycobiome in health and disease, and highlight the importance of maintainingbalance of the GI microbiota. Additionally, taking into consideration recent next generation sequencingdata, we provide insight into potentially new therapeutic approaches in the treatment of IBD throughthe use of antifungals and/or probiotics aimed at establishing and maintaining a healthy balance of theGI total microbial community including fungi and bacteria.