While the Nuclear Pore Complex’s (NPC) canonical function is to act as a selective barrier across the Nuclear Envelope (NE) and regulate nucleocytoplasmic traffic, recent studies have shown that Nucleoporins (Nups), the 30 proteins that comprise the NPC, are also involved in chromatin-related processes such as the regulation of genes and chromatin architecture. However, whether individual Nups bind and regulate distinct types of chromatin remains poorly understood. To decipher how Nups are involved in different aspects of chromatin regulation, we conducted ChIP-seq analysis of three Nups in two different D. melanogaster cell lines. Specifically, we mapped chromatin binding of Elys, which possesses a chromatin-binding domain, and of two stable Nups, Nup93 and Nup107, which are members of the NPC inner and outer ring sub-complexes, respectively. We found that Elys is common to the majority of both Nup107 and Nup93 binding sites, indicating that may Elys act as a link between interphase chromatin and stable Nups. Contrary to expectation, we found that Nup93 and Nup107 share only a small number of their binding sites and exhibit highly unique binding patterns. Nup107 is enriched at transcription start sites and active chromatin, while Nup93 overlaps with Polycomb silenced chromatin regions. Importantly, we found that Nup93 interacts with members of both PRC1 and PRC2 complexes and is enriched for the most tightly regulated Polycomb binding domains. Importantly, we found that Nup93’s association with Polycomb domains is functional as Nup93 plays a role in both the spatial folding of Polycomb domains and in Polycomb mediated gene repression. Furthermore, we found that stable Nup binding sites can be found within LADs indicating that NPCs are present within currently defined LADs and that the genome colocalizes linearly along the nuclear envelope. Together, our findings suggest that different NPCs bind to distinct chromatin regions via interactions with different stable Nups and that a subset of Polycomb domains are bound and regulated by Nup93.