Epizootic shell disease (ESD) is a recently described form of shell disease affecting the American lobster (Homarus americanus, H. Milne Edwards). The disease has caused serious losses to the American lobster fishery. Affected lobsters are unmarketable as a result of the severe biofouling present on the carapace surface. Eukaryotic micro- and macro-organisms have been observed in ESD lesions, but their identity and the extent of their presence has not been determined. We amplified 18S rRNA gene sequences from eukaryotic communities in ESD lesions and separated them for sequencing using denaturing gradient gel electrophoresis. The diversity of the eukaryotic communities was surprisingly high, with as many as 7 different organisms detected in a number of lesions. The eukaryotes identified belonged to broad taxa, including Metazoa, Protozoa, and Fungi. Some organisms were detected in a number of samples and may have a specific role in ESD lesion development and biofouling, including the nematode Geomonhystera disjuncta, various barnacles, stramenopiles, and bryozoans. Aside from G. disjuncta, the other eukaryotes were only sporadically detected and were, therefore, likely opportunistic. However, G. disjuncta is a known bacterivorous nematode; thus, it, too, is likely opportunistic because high numbers of bacteria are known to exist in ESD lesions. Although the eukaryotic organisms in ESD lesions are likely secondary invaders, they may contribute significantly to the biofouling of the carapace seen in severe ESD.