Bovine mastitits caused by the colorless, yeast-like alga Prototheca zopfii is a serious and complex condition that results in heavy economic losses in the dairy industry, both through a substantial reduction in milk production and culling of infected animals. Based on the 18S rDNA sequence analysis, genotype-specific PCR assays have recently been developed to differentiate within the species P. zopfii three distinct P. zopfii genotypes (1-3), of which P. zopfii genotype 3 has been considered a new species P. blaschkeae sp. nov. The purpose of this study was to employ the newly-devised molecular approach for the detection of the two P. zopfii genotypes and P. blaschkeae sp. nov. among bovine mastitis isolates from Poland. This study is the first to provide molecular characterization of Polish P. zopfii mastitis isolates. It also gives the first description of bovine mammary protothecosis due to P. blaschkeae in Poland, as evidenced by genotypical, microbiological, and electron microscopy findings.