The mitochondrial population is heterogeneous in eukaryotic cells. The heterogeneity of mitochondria can be defined as a variation in certain characteristics of mitochondria within the same or different cells. Differences between mitochondria are possible to classify as nongenetic (structural, morphological, and bioenergetic features) or genetic (differences in mtDNA copy number or sequence). Changes in mtDNA sequence are reflected in the phenomenon of heteroplasmy, which is the presence of several mitochondrial genotypes in a cell or an organism. The review considers the features of the organization and dynamics of the chondriome in plant cells compared with cells of other taxonomic groups of organisms. Particular attention is paid to the factors and mechanisms that lead to mitochondrial heterogeneity, heteroplasmy in plants, possible functional specialization of mitochondria, and the role of these processes in the whole organism. A great number of data indicate that the heterogeneous state of mitochondria in the cell is due, among other factors, to the species-specific features of the mitochondrial dynamics processes that are responsible for the homogeneity of the mitochondrial population.