The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts undergo binary fission and equally separate their DNA into the daughter organelles as observed in prokaryotes. Furthermore, ribosomes in both mitochondria and chloroplasts are sensitive to antibacterial antibiotics.

Prokaryotic genomes have millions of base pairs and thousands of genes; mitochondrial and chloroplast genomes, except in a few plants, are much smaller with numbers of base pairs in the thousands with a few hundred genes. This difference in genome size occurred because, during evolution, significant parts of primitive mitochondrial and chloroplast genomes were exported to the nucleus. This export of genes made them dependent on the nuclear genome for the supply of some of the proteins required for their biogenesis.

The different evolutionary paths taken by animals and plants have resulted in significant differences between genomes of animal mitochondria and plant mitochondria and chloroplasts. Animal mitochondrial genomes are smaller than plant mitochondrial and chloroplast genomes. Also, similar to most prokaryotic genomes, animal mitochondrial genomes do not carry any introns. However, introns are present in the genomes of both plant mitochondria and chloroplasts. Compared to mitochondrial genomes, chloroplast genomes show less variation in size and structure and also contain more genes. For example, the number of genes present in the chloroplast genome of Arabidopsis thaliana is almost double of the genes present in its mitochondrial genome. Furthermore, chloroplast genomes are more similar to their prokaryotic counterparts than the mitochondrial genome as they are similar in their regulatory sequences and arrangement of many gene clusters.