The Pig-nosed Turtle Carettochelys insculpta (Testudines; Cryptodira; Carettochelyidae) is the sole living representative of the Carettochelyidae. The phylogenetic position of C. insculpta within Testudines has not yet been determined unequivocally. To address this issue, we sequenced the whole mitochondrial DNA (mtDNA) of C. insculpta using the long-and-accurate PCR (LA-PCR) method. The results show that the length of C. insculpta mtDNA is 16 439 bp and its structure is conserved compared to those of other turtles and other vertebrates except the NADH4 gene beginning with an ATC start codon. The 3′-side of the control region in mtDNA has two tandem repeat motifs, each consisting of nine 5′-CA-3′ units and sixteen 5′-AT-3′ units. To assess the phylogenetic position of C. insculpta, Maximum parsimony (MP), Maximum likelihood (ML) and Bayesian (BI) analyses were conducted based on complete mtDNA from 22 taxa. MP analyses robustly supported that the earliest phylogenetic tree splits separated into three basal branches: the Pelomedusidae (Pelomedusa subrufa), the Carettochelyidae (C. insculpta) and an assemblage of 18 cryptodiran turtle species; while ML and BI analyses suggested that Carettochelyidae and Trionychidae formed a clade, and that this clade was the sister taxon to all other cryptodiran turtles.