Mitochondria
are the site of manufacture of ATP by aerobic processes. They are more closely
related to a group of bacteria than they are to the eukaryotes which harbour
them. 
It is now widely accepted that mitochondria were acquired by a symbiotic event (see discussion of plastids), whereby the ancestral bacterium was taken up or parasitized a eukaryote, and was never rejected. This probably happened over 2 billion years ago. With the passage of time, an intimate association developed. The responsibility for the maintaining the genome coding for mitochondrial proteins shifted to the nucleus.
Much of the enzymatic machinery for respiration lies in the folds of the inner of the two mitochondrial membranes. These are the cristae. Cristae have diferent appearances in different types of protists. The mitochondria of the euglenozoa have flattened cristae, with narrow necks attaching them to the inner mitochondrial membrane. They are therefore like table-tennis bats in appearance. In other protists they may be flat plates or tubular.
In this micrograph, the microtubules which support the mouth (2) lie alongside the mitochondrion.
The kinetoplast is an organelle found only in the mitochondria of kinetoplastid flagellates. It is formed of one or more aggregates of DNA. As is shown in the drawings of bodonids, they may take on diferent appearances. In most kinetoplastids, a single large aggregate forms near the base of the flagella. Sections through the kinetoplast show its fibrillar nature.

When the DNA of the mitochondrion is extracted, it does not form a simple circle typical of most mitochondria, but is a tangled collection of small loops all linked to a loop of DNA.

Because kinetoplasts are only found in kinetoplastid flagellate, they provided much hope that it might be possible to control sleeping sickness and leismanises by developing a drug which would render the kinetoplast DNA dysfunctional. Unfortunately, some natural and laboratory strains of trypanosomes may lack the kinetoplast.