Nuclei in dry Arabidopsis thaliana seeds are very small and have highly condensed chromatin. Nuclear shrinkage and chromatin compaction occur during seed maturation and have been shown to be independent, developmentally controlled processes. To confirm this genetically, we studied chromatin compaction in a mutant of the seed developmental regulator ABA INSENSITIVE 3, and in a double mutant of the nuclear matrix proteins LITTLE NUCLEI 1 and 2. Our results indicated that the nuclear shrinking and chromatin condensation during seed maturation can be genetically uncoupled, confirming that these are independent processes. In addition, we demonstrated that transcript levels of siliques toward the end of seed maturation are comparable to those in vegetative tissues, despite the highly compacted chromatin, small nuclear volume and low hydration status of seeds.