Malignant mesothelioma is increasing in incidence worldwide, including in Japan. However, the accurate pathologic diagnosis of pleural or peritoneal mesothelioma (PM) is sometimes difficult if adequate histologic and immunohistochemical analyses are not undertaken. The aim of this study was to identify a useful antibody panel for distinguishing PM from ovarian serous papillary adenocarcinoma (SC). We obtained 29 PMs (23 epithelioid mesotheliomas and 6 biphasic mesotheliomas) and 20 SCs from our surgical pathology files. Immunohistochemical analysis was undertaken using 13 commercially available antibodies. No significant sex differences in antigen expression among the 29 PMs were observed. The results identified calretinin and thrombomodulin as positive markers and Ber-EP4, MOC-31, CA19-9, and estrogen receptor as negative markers with relatively high sensitivity and specificity for the differential diagnosis of PM and SC. The combination of these positive and negative markers may contribute to accurate diagnosis and adequate therapy for PM and ovarian SC.