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Liriodendron tulipifera L. is easily recognized by its heart-shaped of leaves and can grow up to 60 meters in North America. In this study, we presented second complete mitochondrial genome of L. tulipifera to understand intra-species variations. Its length is 156,387 bp and contains 66 genes (42 protein-coding genes, three rRNAs, and 21 tRNAs). The overall GC content of the mitochondrial genome is 43.5\%, 365 single nucleotide polymorphisms (SNPs; 0.07\%), and 2117 insertions and deletions (INDELs; 0.38\%) are identified. Most of INDELs are from 1980 bp deletions on this mitochondrial genome. Phylogenetic trees show that intra-species relation in both Liriodendron and Arabidopsis shows are clustered tightly in each clade. In addition, monocots and eudicots are positioned in different manner from classical plant taxonomy, requiring more researches.