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The shift from hunting and gathering to farming is one of the most important transitions in human history. Pig domestication has long been an issue of interest in archaeology and genetics. As the real-time carrier of the genetic information for dead or extinct animals, ancient DNA provides continuous molecular evidence for tracing the history of domestication. We collected 30 Late Pleistocene wild boar fossils from three caves in Guangxi Zhuang Autonomous Region (Guangxi ZAR), Southern China. Through the use of the fragmented ancient DNA sequences and the homologous sequences of both domestic pigs and wild boars across Asia and Europe, we reconstructed phylogenetic trees of the pig family. The results show that most wild boar individuals from Guangxi have a closer phylogenetic relationship to Asian pigs than European ones. The data provide additional geographic and temporal evidence for a genetic continuity between ancient Chinese wild boars and the domestic pigs. Moreover, we obtained preliminary evidence for genetic similarity between the ancient wild boar in Guangxi and the European pigs. We suggest that further ancient DNA investigation of the Chinese wild boar samples is essential for revealing the historical process of pig domestication. [ABSTRACT FROM AUTHOR]