Hybridization between species or diverged populations may lead to individuals with mixed ancestry that are reproductively isolated from their parents, resulting in species formation. Although the genomic outcomes of speciation by hybridization have been extensively investigated, the dynamics of organelle genome evolution and its contribution to speciation in this context remain to be fully investigated. Here we study the dynamics of mitochondrial evolution during hybrid speciation in species where mitochondrial genomes are bi-parentally inherited. We used North American lineages of Saccharomyces paradoxus that are characterized by partially overlapping distributions and distinct responses to environmental conditions that suggest ecological divergence. The lineage SpC* was recently discovered and shown to be an incipient species that resulted from hybridization between the sister lineages SpC and SpB in their overlapping distribution. Analysis of three SpC* mitochondrial genomes revealed two mostly SpC-like haplotypes and one mostly SpB-like haplotype that all contain introgressed regions, showing extensive mitochondrial genetic admixture in the process of hybridization. These data suggest that mitochondrial genomes readily recombine in hybridizing lineages. We tested this hypothesis experimentally by analyzing the mitochondrial genomic haplotypes of experimental F1 SpB-SpC hybrid strains and showed that frequent recombination events occur within few generations. We are currently examining the adaptive potential of the new mitochondrial haplotypes produced by recombination. Our results show that mitochondrial genomes recombine in hybridizing species where mitochondria are bi-parentally transmitted.