Horizontal Gene Transfer (HGT) in eukaryotic plastids and mitochondrial genomes is common, and plays an important role in organism evolution. In yeasts, recent mitochondrial HGT has been suggested between S. cerevisiae and S. paradoxus. However, few strains have been explored due to the lack of accurate mitochondrial genome annotations. Mitochondrial genome sequences are important to understand how frequent these introgressions occur and their role in cytonuclear incompatibilities and fitness. In fact, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by cytonuclear incompatibilities. In this study, we have explored the mitochondrial inheritance of several worldwide distributed Saccharomyces species isolated from different sources and geographic origins. We demonstrated the existence of several recombination points in the mitochondrial region COX2-ORF1, likely mediated by the transfer of two different types of ORF1 (F-SceIII), encoding a free-standing homing endonuclease, or mostly facilitated by A+T tandem repeats and regions of integration of GC clusters. These introgressions were shown to occur at intra- as well as at interspecific levels. This suggest a complex model of Saccharomyces evolution which involve several ancestral hybridization events in wild environments.