On the basis of the pulsed field gel electrophoresis (PFGE) technique, molecular karyotypes in Amoeboaphelidium protococcarum (the endotrophic parasite of chlorophycean algae, which combines protozoon- and fungus-type characters) were determined. Molecular karyotypes in the strains X1, X5, and X31, which differ in the host range and originate from Western, Central, and Eastern Euro-Asia respectively, demonstrate the intrageneric polymorphism - from 7 to 13 chDNA bands - with the estimated molecular size of 0.3-2.2 Mb were resolved, and the genome size was determined to be between 7.4 and 10.2 Mb. The molecular karyotype pattern in A. protococcarum is different from that in Protozoa. The low-grade distinction in molecular karyotypes between X1 and X5, on one hand, and high-grade distinction between X1/X5 and X31, on the other hand, makes it possible to place X31 in a separate taxon.