Horizontal Gene Transfer (HGT) in eukaryotic plastids and mitochondrial genomes is frequently observed, 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. In fact, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by these 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 recombination hotspots in the mitochondrial region COX2-ORF1, likely mediated by the transfer of two different types of ORF1, encoding a free-standing homing endonuclease, or facilitated by AT tandem repeats and GC clusters. These introgressions were shown to occur both at intra- and interspecific levels. Based on our results we proposed a model which involve several ancestral hybridization events among Saccharomyces strains in wild environments.