Mitochondria are interesting little beasties. They exist in most eukaryotic cells, and are used to generate most of the ATP - used as fuel - for those cells. But they have their own genome - so in humans, for example, they aren't coded by the DNA in our chromosomes. The mitochondrial genome actually has similarities with bacterial genome. For this and various other reasons, the endosymbiotic theory has come to dominate evolutionary biology, at least in the context of the appearance of mitochondria. This suggests that mitochondria were originally prokaryotic (bacterial-type) cells that ended up in a symbiotic relationship with eukaryotic cells. Some people have elevated this to the status of a "fact" about evolution.
However, some people aren't convinced. Albert de Roos wrote a critique of the theory on Telic Thoughts, recently, and has started his own website, which hypothesises that mitochondria arose from within eukaryotic cells. If your interest in science extends to beyond the posturing that normally takes place between the pro- and anti-darwin lobby, you might enjoy this debate.