Three complete mitochondrial DNA (mtDNA) control regions (CRs) of Chelodina rugosa (Ogilby, 1890), Chelus fimbriata (Schneider, 1783), and Podocnemis unifilis (Troschel, 1848) were firstly determined using Long-PCR method and the length were 1,016 bp, 1,149 bp, and 985bp, respectively. Together with CRs of Pelomedusa subrufa (Bonnaterre, 1789) and nearly complete CR of Podocnemis expansa (Schweigger, 1812) obtained from GenBank, the structural and evolutionary characteristics of mtDNA CRs in pleurodiran turtle were analyzed in this study. We identified three functional domains (TAS, CD, and CSB domains) as well as their conservation sequences (TAS, CSB-F, and CSB-1) according to their homology to those of other turtles. Within the TAS domain, an interrupted poly-C stretch was found in C. rugosa, C. fimbriata, and P. subrufa, which also exists in the published mt DNA CRs of Chrysemys picta (Schneider, 1783), Trachemys scripta (Thunberg in Schoepff, 1792), and Trionyx triunguis (Forskål, 1775). The analysis of the origin for the poly-C sequences in TAS domain from six turtles suggested that the poly-C sequences are more related to "goose hairpin" in birds rather than CSB2 in CSB domain. In the CSB domain, CSB2 and CSB3, which were determined in CRs of Cryptodira, were absent in Pleurodira CRs, indicating the regulative mechanisms of transcription may be varied in both two suborders and the lack of CSB2 and CSB3 could be proposed as one of diagnostic characters between Pleurodira and Cryptodira at molecular level. As for CR of other cryptodiran turtles, variable number of tandem repeats (VNTRs) in the 3' end of the CRs was found in the five pleurodiran turtles. Interestingly, the long repeated motifs from each species could form stable stem-loop secondary structures, suggesting that the repeated sequences may play an important role in regulating replication of the mitochondrial genome in Pleurodiran, and the secondary structures of VNTRs may provide some potential information in phylogenetic inference.