I examined genetic variation for two populations of Black-crowned Night Herons using a 467 base pair region of the mitochondrial DNA. One population inhabits an environment highly impacted by industrial waste, heavy metals, and urbanization; while the other, a reference population, comes from a contaminant-free area. I observed a total of 10 haplotypes, three of which the two populations share. One individual from the contaminated site was ostensibly heteroplasmic. I found no evidence of significant genetic differentiation between the two populations. Coalescent simulation results provided evidence that both populations have undergone or are currently undergoing population expansion. The results of the biological marker I developed showed a high diversity for the ND-6 gene, making it a useful biomarker of population effects.