AbstractBrown bullhead were sampled from contaminated and relatively pristine sites to determine whether there was any association between genetic diversity and site contamination. Nine sites were sampled in the lower Great Lakes: five from Areas of Concern (identified by the International Joint Commission as having significant environmental degradation) and four from relatively clean areas of similar habitat type. Genetic variation was surveyed in the mitochondrial genome using restriction fragment length polymorphisms. Sixteen restriction enzymes were used to identify 42 distinct mitochondrial DNA haplotypes among 163 fish. Eight pairwise comparisons of populations at contaminated vs. clean sites showed that genetic diversity estimates were always lower in populations from contaminated sites. The most parsimonious explanation is that reduced diversity is a result of stochastic reductions in population size that have culled much of the genetic diversity from populations. Although contaminated sites support large populations of brown bullhead, historical environmental degradation at these sites may have reduced population size in the past, resulting in reduced present‐day genetic diversit
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