Sites adjacent to (near-field) and distant from (far-field) oil-drilling platforms were sampled for harpacticoid copepods at two locations in the northern Gulf of Mexico off the coast of Louisiana, both at depths of ≈ 1100 m. The sites were located at Garden Banks Area Block 602 (GB 602) and Mississippi Canyon Area Block 292 (MC 292). Near-field sites at both locations were characterized by large numbers of a single undescribed species of harpacticoid copepod, Bathycletopsyllus sp., but this species was essentially absent from far-field sites. We sequenced a 710 bp portion of the mitochondrial cytochrome c oxidase subunit I gene (COX I) to analyze the genetic diversity and population structure of Bathycletopsyllus sp. at the two platforms, and to determine if the harpacticoids examined were either a single species, or a complex of cryptic species. We found that divergence at the COX I gene (maximum 1.6%) was within the range observed for intraspecific variability in previously-studied species of harpacticoid copepods that were well-characterized taxonomically. Thus, the two samples analyzed here were a single species and not a complex of cryptic species. In addition, there was significant genetic heterogeneity between the two samples, suggesting limited gene flow between the two sites. This was expected given the low dispersal potential typical of harpacticoids and the distance between the sites (407 km). Lastly, haplotype diversity and nucleotide diversity were both low in the GB 602 sample, giving a nominally-significant departure from a pure neutral model. This result could indicate the occurrence of selective sweeps, temporal population size variation or other processes not included in the neutral model. In contrast, haplotype diversity and nucleotide diversity were both higher in the MC 292 sample than at Garden Banks, and there was no detectable departure from neutrality. For both samples, diversity at the haplotype and nucleotide levels were within the range seen in shallow-water harpacticoid species inhabiting both uncontaminated and contaminated muddy sediments, so there was no evidence for pollution related effects in the present study.