Previous studies examining the population structure of aquatic organisms have been based generally on behavioral traits, morphological traits and allozyme studies. DNA sequence analysis of the mitochondrial cytochrome oxidase I gene may also be of use to study population structure. Thus, a study investigating the genetic variation within and among seven populations, distributed from Quebec to New York, of the freshwater copepod Diaptomus leptopus was conducted.  Variation among populations was shown in both the nucleotide sequence and the observed haplotype frequencies. These results indicate that the populations may differ. The phylogenetic tree obtained reveals that most of the individuals studied are most similar genetically within their population and that there are varying degrees of differentiation among populations. Most of the nucleotide substitutions are synonymous and a majority of the base changes occur at the third codon position. The amino acids that do change in the calanoid copepod occur at sites which are variable for other organisms sequenced. Hence, these sites are not thought to be important for the maintenance of the protein structure and function. Therefore, these results suggest that the gene product is not altered and the differences seen, in the mtCOI gene, among the populations, studied here, may be selectively neutral. The results obtained need to be supported by more individuals and genes studied, examination of historical aspects of population distribution and further analyses.