Nuclear Pore Complexes (NPCs) are large macromolecular assemblies embedded into the nuclear envelope (NE). Their main function is to mediate the selective nucleocytoplasmic transport of macromolecules, although they are involved in other processes such as chromatin organization, and DNA repair. NPCs are organized into subcomplexes composed of repetitions of about 30 highly conserved nucleoporins (NUPs). The NUP107–160 complex is in the outer ring and is conserved between distantly related eukaryotes such as yeast and mammals. Here, we are going to focus on two Arabidopsis mutants deficient for this subcomplex: nup160 and nup96, also known as suppressor of auxin resistance1 (sar1) and sar3, respectively. NUP160 and NUP96 are critical for the nucleocytoplasmic transport of mRNAs and play important functions in auxin signalling, plant growth, and flowering time regulation, as well as in immune defence and cold stress tolerance. In the context of our global study about the possible role of NPCs during meiosis, we decided to explore the potential function of NUP160 and NUP96 during this cell division because the corresponding mutants show reduced fertility. The results of our study have demonstrated that meiosis is altered in a percentage of the meiocytes from these mutants, which would explain the reduction in the number of seeds. Our observations have revealed that the alteration of the NUP107-160 complex causes problems related to chromatin instability with abnormalities associated with condensation and fragmentation. The possible origins of these problems will be discussed.