The functions of mitochondria depend on precise interaction between nuclear and cytoplasmic genomes. Non-balance of mtDNA has been reported in most nuclear transfer embryos and offspring. The reason of the degradation of donor mtDNA is still not clear. To further investigate the mechanism, in this study, we designed an experiment as follows. Two fibroblast cell lines sharing same nuclear genome but different mitochondria genome backgrounds, namely cells from ear tissues of cloned bovine and its donor, were choose as donor cells and introduced into enucleated rabbit oocytes. Similar developmental potential was observed in cloned bovine-rabbit (clone group) and bovine-rabbit (non-clone group) embryos. Real-time PCR assay showed that, in non-clone group, bovine mtDNA decreased during the development of reconstructed embryo, and that a sharp decrease was detected at the blastocyst stage. In clone group, bovine mtDNA decreased slightly, and the abrupt reduction of donor mtDNA did not occur during preimplantation development. In addition, an obvious increase in rabbit mtDNA was observed in both groups at the blastocyst stage. Our results demonstrate that: 1) the fates of donor mtDNAs in bovine-rabbit and cloned bovine-rabbit reconstructed embryos were different; and 2) recipient mtDNAs replicate at blastocyst regardless of the difference of donor cells.