The centromere is the kinetochore-forming region during mitosis, and eukaryotes have two patterns for centromere distribution in the interphase nuclei: the Rabl and the non-Rabl orientation. In the Rabl orientation, centromeres cluster on one side of the nucleus, whereas they are randomly scattered in the non-Rabl orientation. The molecular mechanism underlying these configurations and the biological significance of proper centromere distribution during interphase is still unknown. Arabidopsis thaliana takes the non-Rabl orientation, and we have found that this arrangement is cooperatively regulated by condensin II and the linker of the nucleoskeleton and cytoskeleton (LINC) complex. In this study, we focused on the nuclear pore complex (NPC) to test whether it is a new factor involved in centromeres arrangement. The NPC comprises about 30 nucleoporins (Nups) and is well known to regulate nucleo-cytoplasmic transport. In addition to this canonical function, recent studies in yeast and animals revealed that NPCs are also involved in gene expression, transcriptional memory, and chromatin organization via interaction with chromatin. However, little is known about these functions in plants. We observed centromere localization in 12 different nup mutants and found that centromeres showed abnormal distribution in 5 nup mutants. In addition, the interaction between Nup and the LINC complex was confirmed by co-immunoprecipitation, and the genetic analysis revealed that Nup and the LINC complex function in the same pathway on the centromere arrangement. These results suggest the novel function of plant Nup proteins as regulatory factors of centromere arrangement.