The pink shrimp, <i>Farfantepenaeus duorarum</i>, is one of the most important shrimp species commercially harvested along the Gulf and Atlantic coasts of the US. In this study we developed a mitochondrial marker suitable for population studies of the species. A 611-617 bp hypervariable portion of the AT-rich region of the mt genome was amplified and sequenced. The 617 bp long consensus sequence contained 15 polymorphic insertion/deletion sites and 165 polymorphic substitution sites. Kimura 2-parameter distances ranged from 0.00 to 0.06 with a mean of 0.02. Among the 104 sequences, 100 haplotypes were counted if all mutations were included. If transitions were omitted, 34 haplotypes were observed. The results indicate that the hypervariable portion of the AT-rich region may be an effective marker for revealing the genetic structure of the pink shrimp off the southeast US.