The Atlantic gollath grouper is a critically endangered species that inhabits estuarine and reef environments and is threatened primarily by fishing activities and habitat destruction. Despite the urgent need for protection, its genetic conservation status remains unknown. The aim of the present study was to evaluate the gene flow among the populations of the species along the coast of Brazil based on the control region of the mitochondrial DNA. The results indicate low haplotype diversity and very low nucleotide diversity. They also show that the genetic diversity of the species varies considerably along the coast and that this finding may be especially important for the identification of priority areas for its conservation. The results of this study suggest that, though it may be incipient, the observed genetic structuring must be taken into account in order to prevent potential problems, such as out-breeding depression, in the management of wild stocks.