Malignant peritoneal mesothelioma represents less than a quarter of all malignant mesothelioma cases. Malignant mesothelioma can be classified based on morphology into epithelioid, sarcomatoid, or mixed types. Peritoneal epithelioid mesothelioma with predominant clear cell features is very rare and mimics various malignancies posing a diagnostic challenge. Here we report a rare case of primary peritoneal mesothelioma with clear cell features presenting with liver masses. A 68-year-old man who had multiple liver nodules on imaging was admitted for worsening abdominal pain. He complained of intermittent abdominal pain for more than 10 years. Longitudinal follow-up of the patients' abdominal images over 10 years showed slowly progressive liver lesions. Microscopic examination of resected tumors revealed pleomorphic epithelioid neoplasm with clear cytoplasm, distinct cell borders, optically clear chromatin, and prominent nucleoli embedded in a vascular stroma. Immunostaining showed that the tumor cells were positive for AE1/3, vimentin, carbonic anhydrase IX, TFE1/33, and Gata3, whereas they were negative for PAX-8, arginase-1, hepatocyte specific antigen, inhibin, S100, DOG1, CD117, CD31, TTF-1, p63, smooth muscle actin, and HMB45. CancerType ID testing favored the diagnosis of mesothelioma with 90% probability, a diagnosis that was further confirmed by calretinin and WT1 positivity. Foundation genomic testing showed VHL Y98fs*24 mutation, a unique genetic mutation that, to our knowledge, was never described before. In summary, this is a rare case of primary peritoneal mesothelioma with clear cell features presenting as liver masses. The tumor had a unique genetic mutation and behaved in an indolent manner in contrast to what is commonly seen in mesotheliomas.