Nucleoporins (nups) compose the structure of the nuclear pore complex (NPC) of all cells, but several studies have illuminated nucleoporins’ additional roles in development and the cell cycle. However, a comprehensive study of nup expression in embryonic development has not yet been reported. We synthesized antisense probes for all nup genes and used whole-mount in situ hybridization techniques to determine the expression pattern of all members of the nup family of genes at three different developmental stages in Xenopus tropicalis. We found that the expression of nups was not ubiquitous in embryos, but was localized to specific and distinguishable anatomical structures at all three stages tested. We also found that the expression patterns for nups within the same subcomplexes were not necessarily identical. Thus, nup expression is subject to a significant level of regulation during development. These results provide new information for functional studies of nups to unravel their roles in embryonic development.