Plants possess compartmentalized genomes that are distributed in the nucleus and in two organelles: the mitochondria (mt) and plastids (pt). The crucial functions of these organelles require interaction between products encoded by the organelle genome and the nucleus. Hence, coadaptation contributes to the evolution of plant genomes, leading to a cooperative coevolution between interacting gene products that are encoded in different compartments. In addition, the different modes of inheritance between the Mendelian nuclear genes and uniparental organelles create a genomic conflict that also contributes to shape the evolution of some mt and nuclear genes: those involved in cytonuclear male sterilities. Pentatricopeptide repeat proteins have been involved in the evolution of the mt-nuclear conflict, but are also suspected to participate in the cooperative coadaptation between the nuclear compartment and organelle genomes. Several lines of evidence indicate that organelle genetic variations contribute to plant adaptation to their environment. So far, very few studies have identified potentially adaptive organelle variants. Nevertheless, it is very likely that cytonuclear coadaptation interferes with cytoplasmic adaptation to the environment. Both phenomena must therefore be considered in future work aiming at a better understanding of the evolution of organelle genes and adaptive component.