Mitochondria, the organelles involved in cellular respiration and energy generation (adenosine triphosphate [ATP]), regulate essential cellular activities. They are primarily associated with major molecular functions, including cell division, growth, damage repair, and stress tolerance. The molecular mechanisms executing these functions deploy macromolecules such as hormones, metabolites, amino acids, proteins, reactive oxygen species (ROS), and superoxides and contribute to signaling pathways. Mitochondria play an important role in metabolic and stress-responsive signaling pathways, and the signaling molecules associated with those pathways include many, but salicylic acid, jasmonic acid, brassinosteroids, ethylene, auxin, gibberellin, and cytokinin are the most studied. As the powerhouses of the cell, mitochondria maintain homeostasis in the cellular environment through the production of ATP, generation of ROS, and scavenging the excess ROS produced in the cytoplasm. All these critical cell functions are regulated by the limited number of mitochondrial genes and the nucleus through retrograde and anterograde signaling. Cyto-nuclear communication regulates growth, development, and stress. Mitochondrial role in male sterility and its application to plant breeding have garnered researchers’ attention to produce pure, cost-effective, and productive hybrids and combine desirable agronomic traits. Study of mitochondrial genes conducted in diploid, tetraploid, and hexaploid wheat provided important insights on its evolution, development, and defense. Mitochondria have a much smaller genome and have limited number of genes relative to the nucleus. They have repetitive DNA sequences with large introns and share some homology with the nuclear genome. This provided insight into the evolutionary theory that most mitochondrial genes were transferred to the nucleus over time. As major organelles have their own genome, mitochondria contribute to cell homeostasis and crop improvement. Although many details are yet to be resolved, we review here mitochondrial genes, structure, and function and some pioneering work on bread wheat and its wild relatives.