The leading hypothesis on the ancestor of domestic goats (Capra hircus) is that it is the wild goat called the bezoar or pasang (Capra aegagrus). To verify this hypothesis, we sequenced and compared the cytochrome b gene of mitochondrial DNA from six domestic goats and bezoar. A further sequence for the markhor was taken from the database. In total we detected 51 nucleotide substitutions among the domestic goats, bezoar and markhor. However, only one specific nucleotide substitution was found between the domestic goats and the bezoar. On the other hand, 43 nucleotide substitutions were specific for the markhor. This result suggested a close relationship between the domestic goats and the bezoar. A neighbor-joining and parsimony phylogenetic tree constructed using the sequences showed that the domestic goats and the bezoar belong to the same cluster, while the markhor showed a distinct cluster separate from that of the domestic/bezoar cluster. This result was confirmed by trees based on the sequence of the mitochondrial displacement loop regions. These results suggest that the strongest candidate for a matriarchal ancestor of domestic goats is the bezoar.