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The purposes of this study were to investigate single strand conformation polymorphisms (SSCP) in the D-loop region of pig mitochondrial DNA (mtDNA) and to determinate their association with the reproductive traits of meishan pigs. A total of four types of band patterns, designed SSCP band pattern A, B, C and D, were identified. A type of SSCP band pattern was present in all European-American breeds, but not in East Asian breeds. This result showed the diversified sequence in the D-loop region between European-American and East Asian populations. Two types of band patterns, B and C, were found in Meishan pigs. The average body weight at day 21 of piglets from B type dams was significantly heavier than the body weight of C type (p < 0.05). We also tested whether the SSCP patterns would be suitable for paternity testing in a family group and found that bands of all the offspring were derived from their maternal parent. Therefore, we conclude that SSCP may be a marker for identification of maternal ancestors.