In this study we describe the first complete mitochondrial sequence of the Critically Endangered Smalltooth Sawfish Pristis pectinata. It is 16,802 bp in length and contains all 37 genes found in typical vertebrate mitogenomes. The nucleotide composition of the coding strand is 31.1% A, 26.0% C, 13.1% G and 28.9% T. There are 29 bp overlaps and 38 short intergenic spaces dispersed in the mitogenome. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were found in the protein-coding genes. The length of the 22 tRNA genes range from 67 bp (tRNASer2) to 75 bp (tRNALeu1). The control region is 1102 bp in length with high A + T (62.0%) and poor G (13.5%) content.