We evaluated stock structure and demographic
(population) history of red snapper (Lutjanus campechanus)
in the northern Gulf of Mexico (Gulf) via analysis
of mitochondrial (mt)DNA sequences from 360 individuals
sampled from four cohorts (year classes) at three
localities across the northern Gulf. Exact tests of genetic
homogeneity and analysis of molecular variance both
among cohorts within localities and among localities
were non-significant. Nested clade analysis provided
evidence of different temporal episodes of both range
expansion and restricted gene flow due to isolation by
distance. A mismatch distribution of pairwise differences
among mtDNA haplotypes and a maximum-likelihood
coalescence analysis indicated a population expansion
phase that dated to the Pleistocene and probably represents
(re)colonization of the continental shelf following
glacial retreat. The spatial distribution of red
snapper in the northern Gulf appears to have a complex
history that likely reflects glacial advance/retreat, habitat
availability and suitability, and hydrology. Habitat
availability/suitability and hydrology may partially restrict
gene flow among present-day red snapper in the
northern Gulf and give rise to a metapopulation structure
with variable demographic connectivity. This type
of population structure may be difficult to detect with
commonly used, selectively neutral genetic markers.