Objective Assembly whole mitochondrial genome sequence of Rongshui miniature pig (RMP) breed and analysis the structure of mitochondrion based on the next-generation sequecing method. Comparison of phylogenetic relationship and genetic diversity among different pig breeds. Methods We collected peripheral venous blood sample from RMP and constructed two paired-end sequencing libraries. A whole-genome shotgun sequencing strategy and Illumina Genome Analyser sequencing technology were used in our study. Results The mitochondrial genome of RMP consists of 13 protein coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and the length of pig is 16888 bp. The GC content of this pig mitochondrial genome is about 44 %. Based on phlogenetic analysis, population genetic analysis, our findings confirmed that the ancestral cluster in East Asia mainly occurred among Diannan 7# pig, Hainan wild boar, Lanyu and RMP. Conclusion RMP, a typical miniature pig breed in China, is an earlier ancestor than Lanyu pig breed.