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The origin of domesticated pigs is of interest to the general public. Technology to analyze ancient DNA can provide direct scientific evidence to address this question. It has been reported that modern Chinese pigs were domesticated in an independent pattern in the area of the middle and lower reaches of the Yellow River; however, ancient pig samples from the upper reaches of the Yellow River have never been tested. In this study, 14 unearthed ancient pig samples were collected from three archaeological sites in the upper and middle reaches of the Yellow River. Using DNA extraction, PCR amplification and DNA sequencing, these ancient samples were analyzed and compared with gene information from ancient pig samples from the middle and lower reaches of the Yellow River and from modern wild boars and domesticated pigs. We succeeded in generating a 179 bp sequence of mitochondrial D-loop from five ancient pig samples respectively, including three samples from the Qinglongquan archaeological site in Hubei Province and two samples from the Lajia archaeological site in Qinghai Province. Sequence alignment analysis indicated that ancient samples from Qinglongquan and Lajia were sorted into different haplotypes. Compared with previous data from ancient DNAs, modern pig breeds and wild boars, the two Qinglongquan samples shared one haplotype with one sample from the Jiahu site, and the Lajia samples shared a haplotype with four samples from the Gaohong archaeological site and with three samples from the Taosi archaeological site, which are both located in Shanxi Province. The two haplotypes were consistent with the four main types of modern Chinese pigs. The results indicate that pigs in the upper reaches of the Yellow River originated from the same domestic center as the pigs in the middle and lower reaches of the Yellow River did. These findings further our understanding of the origin of pig domestication in China.