In this paper, we sequenced the complete mitochondrial genome of Kallima inachus (Lepidoptera: Nymphalidae: Nymphalinae), which is considered a rare species in China. The genome is 15,183 bp in size. Its gene arrangement pattern was identical with those of Argynnis hyperbius. We compared the mitochondrial genome of K. inachus with that of A. hyperbius. Nucleotide sequence similarity between the two whole mitochondrial genomes was 85.92%, and the relatively low similarity seems to indicate that the two species are distinctly separated on the species level. The information on the mitochondrial genome comparison of the two species is discussed in detail in this paper.

The complete mitochondrial genome sequence of Lacerta agilis was determined in the present paper. The genome was 17,090 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region (CR). The gene composition and order of which was similar to most other Squamate reptiles. The overall base composition of the genome in descending order was 31.29% A, 26. 39% C, 29.01% T and 13.29% G, with a slight AT bias of 60.30%. CR is located between the tRNA-Pro and tRNA-Phe genes and is 1688 bp in length, some tandem repeat sequences and conserved elements (CSB1-3) were found in the control region.

The complete mitochondrial genome sequence of Gekko swinhonis was determined in this paper. The genome was 16,818 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region (CR). The gene composition and order of G. swinhonis were similar to most other squamate reptiles. The overall base composition of the genome in descending order was 31.35% A, 27. 71% C, 26.28% T, and 14.67% G, with a slight AT bias of 57.62%. CR is located between the tRNA-Pro and tRNA-Phe genes and is 1456 bp in length; some tandem repeat sequences and conserved elements (TAS, CSB1-3) were found in the CR.

The complete sequence mitochondrial genome of Takydromus sexlineatus was determined using long PCR and conserved primers walking approaches. The genome was 18,943 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region (CR). The gene composition and order of T. sexlineatus were similar to most other squamate reptiles. All protein-coding genes begin with ATG as initiation codon except COI using GTG. Seven genes (ATP8. ND4L. ND5. Cytb. ND1. COI and ND6) ended with TAA, TAG, AGGA and AGA stop codon, the remaining 6 genes had incomplete stop codons T/TA. The overall base composition of the genome in descending order was 31.48% A, 24.67% C, 30.79% T and 13.05% G, with a slight A + T bias of 62.27%. CR is located between the tRNA-Pro and tRNA-Phe genes and is 3562 bp in length, some tandem repeat sequences, conserved elements (CSB1-3) and termination associated sequences (TAS1-3) were found in the control region.

The 16,585 base pairs mitochondrial genome of Shinisaurus crocodilurus was determined by using PCR amplification and DNA sequencing. To determine the phylogenetic position of S. crocodilurus with related species within Squamata, the phylogenetic tree was reconstructed with the concatenated nucleotide sequences of the 12 heavy-strand-encoded protein genes. Phylogenetic analyses based on maximum parsimony and Bayesian inference methods consistently support that the S. crocodilurus was closely related to the Helodermatidae within a monophyletic Anguimorpha group. And the result here contradicted the monophyly of Varanoidea (Varanidae + Helodermatidae). In addition, the Gekkonidae was found to possess a basal phylogenetic position within squamata and the traditional hypothesis of monophyletic lineages of Iguania and Scleroglossa was not supported in this study.