Abstract Mitochondria are an indispensable component of every plant cell and are inextricably linked to many vital functions. One of their key characteristics is that they have their own genome. This genome, although greatly reduced, encodes several essential genes. While this has been known for decades, until recently it has not been possible to study the mitochondrial genome and its function in detail due to the lack of suitable tools for forward and reverse genetics. This is partly due to the low mutation rate in mitochondria and the lack of methods for direct transformation. A breakthrough came with the use of nuclear encoded transcription activator-like effector (TALE) nucleases (TALENs) for targeted mitochondrial mutagenesis. One of the first applications was to unambiguously show that certain ORFs were causal for cytoplasmic male sterility (CMS). This had previously been beyond our technical capabilities. TALENs are suitable for all plant species amenable to nuclear transformation because they are protein-only and can be imported post-transcriptionally into the mitochondria. Unfortunately, TALEN mutagenesis in plant mitochondria often seems to be associated with large genomic rearrangements. DNA base editors, the latest addition to the toolbox, bypass these side effects and merely introduce point mutations. They are based on TALEs and could only be developed after the discovery of a cytosine deaminase that acts on double-stranded DNA. The possibilities for targeted modification of the mitochondrial genome in plants are developing rapidly. This article aims to show where we stand in this development and what we can expect in the near future.