Genomic content varies over the course of the life cycle in many lineages across the eukaryotic tree of life. Such variation is thought to be widespread in Foraminifera, a microbial lineage within the Rhizaria, as complex nuclear dynamics have been observed in the life cycle of diverse species. Perhaps the most striking example is the elimination of nuclear material, including DNA, which occurs prior to cell division in the uninucleate life-cycle stage of all species that have been examined. This process, termed zerfall, is hypothesized to eliminate DNA that was previously amplified during the life cycle. Here we test this hypothesis by comparing the relative copy number of ribosomal DNA and two protein-coding genes with quantitative PCR before and after zerfall in the cultured foraminifer Allogromia laticollaris strain CSH. Our results reveal higher relative copy number of ribosomal DNA prior to zerfall, while protein-coding loci are relatively more abundant following zerfall. This suggests 1) that like many other eukaryotic lineages, Allogromia differentially amplifies the ribosomal DNA locus, and 2) that zerfall enables Allogromia to reset copy number prior to cell division. Further, these data add to the observation that some lineages of eukaryotes can differentiate germline and somatic genetic material in the context of a single nucleus.