The mitochondrial DNA (mtDNA) control region of common snookCentropomus undecimaliswas investigated for its potential use as a genetic mark or “tag” for evaluating eventual stock enhancement efforts for this species. In addition, the general feasibility of recovering and recognizing a genetic tag from an enhanced wild population was evaluated. Snook mtDNA purified from ripe ovary tissue by ultracentrifugation in CsCl gradients was restriction mapped, and the control region was cloned and sequenced. When different clones from the same fish were compared, the control region was found to contain variable numbers of a 39-base pair (bp) tandemly repeating sequence beginning 26 by from the transfer RNA gene for proline. Further evidence of this variation in repeat number was observed between individuals after comparison of polymerase chain reaction (PCR) products obtained from this region by using native mtDNA preparations. Following the repeats was a nonrepeating sequence of 701-bp in which two distinctive sequences were seen among snook from Tampa Bay. The sequences were such that 406-bp PCR products of the two were each distinguishable after digestion with eitherRsaI orTaqI followed by agarose gel electrophoresis. In testing the general feasibility of a rapid, nondestructive, tag “recovery” protocol, mtDNA extracted from small fin clips from 1,425 individual wild-caught snook was used as a template for PCR amplification of the sequence. Of 882 successful PCR amplifications, 789 digests byRsaI plus 500 byTaqI were clearly scored by simple visual inspection of ethidium-stained agarose gels. Only one of the two sequences was further observed in this number of fish from Tampa Bay. The results highlight the specificity of an mtDNA sequence assay in recognizing a specific haplotype and also demonstrate the feasibility of scanning hundreds of fish for a particular mtDNA sequence that might serve as a genetic tag in hatchery-released fish. We also concluded that the mtDNA control region alone in snook might not contain enough sequence variability within a local population to fully exploit the potential of genetic tagging and that other regions of the mtDNA should be investigated.