The marine coccolithophorid Emiliania huxleyi is an important component of the marine carbon cycle because bloom development results in the export of calcium carbonate from the ocean surface to the abyss. Laboratory and field studies demonstrate significant biogeographical, ecological, physiological and morphological plasticity in E. huxleyi and suggest high underlying genetic variability. Here we describe seven polymorphic microsatellite loci from the E. huxleyi genome and their degree of polymorphism in clonal isolates of different geographical origin. Our results indicate a high degree of genetic diversity within E. huxleyi.