Altered expression of carbonic anhydrase (CA) II is associated with human carcinogenesis. We analysed CA II protein expression in 89 patients with pseudomyxoma peritonei (PMP) and correlated its association against survival. We determined the expression of CA II by immunohistochemistry and then scored the staining results. The correlations of CA II expression with Peritoneal Cancer Index (PCI) and tumour grade were examined. The effect of CA II and tumour grade on survival was investigated. Positive CA II expression was found in 58 patients (65%) and absent in 31 patients (35%). High-grade (HG) morphology was associated with a loss of CA II expression (p = 0.048). The mean CA II immunostaining intensity score was 1.00 ± 1.1 (median 1, range 0-3) for HG morphology and 1.54 ± 1.1 (median 2, range 0-3) for low-grade (LG) morphology. The 5-year overall survival (OS) for those patients with CA II expression was 80% and 59% for those without (p < 0.001). The 5-year OS rates for those patients with HG morphology and positive CA II expression was 72% and 31% for those with negative CA II expression (p = 0.044). This study suggests that the expression of CA II acts as independent prognostic biomarker for survival in PMP.