Microscopically visible chromatin is partitioned into two major components in Arabidopsis thaliana nuclei. Chromocenters on one hand are conspicuous foci of highly condensed 'heterochromatic' domains that contain mostly repeated sequences. On the other hand, less condensed and gene-rich 'euchromatin' emanates from these chromocenters. This differentiation, together with the dynamic nature of chromatin compaction in response to developmental and environmental stimuli, makes Arabidopsis a powerful system for studying chromatin organization and dynamics. Heterochromatin dynamics can be monitored by measuring the Heterochromatin Index, i.e. the proportion of nuclei displaying well-defined chromocenters, or the DNA fraction of chromocenters (Relative Heterochromatin Fraction). Both measures are composite traits, thus their values represent the sum of effects of various underlying morphometric properties. We exploited genetic variation between natural occurring accessions to determine the genetic basis of individual nucleus and chromocenter morphometric parameters; Area, Perimeter, Density, Roundness and Heterogeneity, that together determine chromatin compaction. Our novel reductionistic genetic approach revealed Quantitative Trait Loci (QTLs) for all measured traits. Genomic co-localization among QTLs was limited, which suggests a complex genetic regulation of chromatin compaction. Yet, genomic intervals of QTLs for nucleus size (Area and Perimeter) both overlap with a known QTL for heterochromatin compaction that is explained by natural polymorphism in the red/far-red light and temperature receptor Phytochrome B. Mutant analyses and genetic complementation assays show that Phytochrome B is a negative regulator of nucleus size, unveiling that perception of climatic conditions by a phytochrome-mediated hub is a major determinant for coordinating nucleus size and heterochromatin compaction.