Understanding genetic variation among populations of medically significant pest insects is important in studying vector transmission, disease epidemiology, and disease control. Aedes vexans is a potential West Nile Virus vector with a widespread distribution throughout the world including the continental U.S. and southern Canada. In the present study mosquitoes were collected in 2004 and 2006, in New Orleans. Over 200 adult mosquitoes from various locations in New Orleans and Jefferson parishes were examined using DNA sequences of a portion of mitochondrial NADH dehydrogenase subunit 5 (ND5) gene. A total of 39 and 58 sites were polymorphic, and 67 and 62 haplotypes were observed in each year, respectively. The average haplotype diversity (0.903) in 2004 and (0.943) in 2006 in New Orleans, and (0.887) in 2004 and (0.975) in 2006 in Jefferson, indicates a high level of genetic diversity. This study provides evidence that there are similar levels of nucleotide diversity in 2004 and 2006, therefore there was no impact on genetic diversity due to the hurricane Katrina.