The plant mitochondrial genome is composed of a set of molecules of va
rious sizes that generate each other through recombination between rep
eated sequences. Molecular observations indicate that these different
molecules are present in an equilibrium state. Different compositions
of molecules have been observed within species. Recombination could pr
oduce deleted molecules with a high replication rate but bearing littl
e useful information for the cell (such as ''petite'' mutants in yeast
). In this paper, we use a multilevel model to examine selection among
rapidly replicating incomplete molecules and relatively slowly replic
ating complete molecules. Our model simulates the evolution of mitocho
ndrial information through a three-level selection process including i
ntermolecular, intermitochondrial, and intercellular selection. The mo
del demonstrates that maintenance of the mitochondrial genome can resu
lt from multilevel selection, but maintenance is difficult to explain
without the existence of selection at the intermitochondrial level. Th
is study shows that compartmentation into mitochondria is useful for m
aintenance of the mitochondrial information. Our examination of evolut
ionary equilibria shows that different equilibria (with different comb
inations of molecules) can be obtained when recombination rates are lo
wer than a threshold value. This may be interpreted as a drift-mutatio
n balance.