The deep sedimentary biosphere, extending hundreds of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Little is known about microbial eukaryotes in these habitats, however studies suggest that fungi dominate. Here we compared fungal ribosomal RNA signatures present in sediment core samples from 6 and 95mbsf from Peru Margin site 1229A. Fungal-specific PCR primers were used in this study.