Two emerging concepts in cell biology are the back-and-forth trafficking of receptor proteins and nuclear transcription factors between the nucleus and the cell membrane, and the alternative splicing of messenger RNA to produce similar proteins targeted to different cell sites. Recent evidence suggests that the nucleolus is a dynamic structure whose components may be involved in both types of trafficking. In the nervous system of higher animals, the N-methyl-D-aspartate (NMDA)-specific glutamate receptor has various roles in development and cell communication. It is involved in learning, memory, axonal guidance and nerve regeneration. We have reported earlier that the NR1 subunit of the NMDA receptor is present in the cell periphery and the nucleus of stem cells, neurons and epitheliomuscular cells of the early-evolved cnidarian, Hydra vulgaris (Scappaticci et al., 2004. Cell Tissue Res 316:263-270); it is involved in coordinating hydra's neuroeffector systems (Kass-Simon and Scappaticci, 2003. Hydrobiologia 530/531:67-71; Pierobon et al., 2004. Eur J Neurosci 20:2598-2604; Scappaticci and Kass-Simon, 2008. Comp Biochem Physiol A 150:415-422; Kay and Kass-Simon, 2009. Bio Bull 216:113-129). Here we report immunocytochemical experiments, using a mouse monoclonal antibody raised against the mammalian NR1 receptor subunit, and an in silico genomic and gene expression analysis identifying the homologues in hydra of mammalian NR1 and fibrillarin (FBL) genes, and their expressed proteins. The experiments reveal that the NR1 antibody specifically labels the nucleoli of large and small interstitial cells (stem cells), nematoblasts, neuroblasts, and epitheliomusclar cells; antibody labeling of the nucleolar marker, FBL, confirms the nucleolar localization of NR1 antibody labeling. Genomic analysis reveals that NR1 and FBL genes are conserved in hydra, and suggests that there are at least two NR1 splice variants, one of which contains both nuclear and nucleolar targeting signals. The finding that an NR1 receptor subunit (or a portion of it) appears in nucleoli of hydra cells is unique, and has not been reported for any other organism. Its presence in nucleoli of hydra may signal the existence of a yet-undescribed shuttle mechanism between the cell surface and the nucleous, or the alternative deployment of NR1 splice variants to different cell sites.