Mucormycosis is a fungal infection, which is difficult to treat due to its rapid dissemination and low susceptibility to anti-fungal agents. Peritonitis preceded by gastrointestinal mucormycosis is very rare, and only a few cases have been reported. We present a case of peritonitis and disseminated mucormycosis caused by Mucor circinelloides in an immunocompromised patient. A 59-year-old man, diagnosed with nodal marginal zone B-cell lymphoma, was diagnosed with liver failure due to severe septic shock. A white, woolly cotton-like growth, which was consistent with that of Mucor species, was isolated from ascites and sputum specimens. Targeted DNA sequencing confirmed the isolate as M. circinelloides with 100% identity. Despite anti-fungal treatment, the patient died after four days. This is a rare case of peritonitis and disseminated mucormycosis that was probably preceded by gastrointestinal mucormycosis caused by M. circinelloides, as determined by molecular methods. Accurate and rapid identification of mold using molecular methods might be necessary for early treatment in critical cases, and more cases should be clinically evaluated further.