The nuclear pore complex (NPC) is the sole gateway for molecular transport between the nucleus and the cytoplasm in eukaryotes. The NPC is composed of approximately 30 different kinds of protein components called nucleoporins. The functional structure of the NPC is highly conserved among various eukaryotes. However, the exact mechanisms by which many of the nucleoporins exert their specific functions still remain unclear. The single cell ciliate Tetrahymena has two functionally distinct nuclei, a macronucleus and a micronucleus, and we have discovered that these two nuclei have compositionally distinct NPCs. We initially identified four nucleus-specific Nup98-s and demonstrated that they are required for macronucleus- and micronucleus-specific nuclear transport. More recently we identified two nucleus-specific paralogs of Nup214 and Nup153 and two nucleus-specific transmembrane proteins Pom121 and Pom82. Our findings argue that Nup214, Nup153, and Pom121/Pom82 also act as key molecules for transport machineries to differentiate the two functionally distinct nuclei present in this organism.