Immunohistochemistry (IHC) of bovine cytokeratin combined with periodic acid-Schiff (PAS) was applied to study the pathogenesis, localization and distribution of Prototheca zopfii in bovine mammary protothecosis. The standard immunohistochemical procedure using anti-bovine cytokeratin was employed before and after PAS staining to optimize this combined method. The best results were obtained when IHC procedures were performed first. Most of the epithelial cells reacted strongly with the pancytokeratin antibody. Protothecal cell walls stained well with PAS. Algal organisms were present within the lumen and between the epithelial lining and basement membrane of the affected alveoli, but not inside the positive mammary epithelial cells. This combined staining method resulted in clear alveolar epithelial detail and good contrast between the epithelial cells and algae, and contributed to studying the pathogenesis of P. zopfii in mammary protothecosis.