Abstract: Despite it small size, the rapid evolution of the mitochondrial genome (mtDNA) has significant implications for the evolution of animal populations. Mitochondrial function requires the transcription and translation of the mtDNA-encoded proteins that are essential for aerobic respiration, and all these functions require proteins encoded in the nuclear genome. Consequently, the many interactions between mtDNA and nucDNA favor extensive intergenomic coadaptation. When genetically divergent populations hybridize, coadaptation can be disrupted and lead to mitochondrial dysfunction and reduced fitness (hybrid breakdown). Interpopulation crosses between populations of the copepod Tigriopus californicus show extensive hybrid breakdown due to intergenomic interactions affecting mitochondrial function (manifested in reduced ATP production and increased oxidative damage). Recent work using transcriptomic analyses of hybrid breakdown and local adaptation in Tigriopus will also be discussed.