Understanding the ecology and behavior of different mosquito species (Diptera: Culicidae) is essential for identifying their role in disease transmission cycles and public health risk. Two species of Culex mosquitoes in the northeastern United States, Culex pipiens L. and Culex restuans Theobald, have been implicated in enzootic transmission of West Nile virus (family Flaviviridae, genus Flavivirus, WNV). Despite the difficulty of differentiating these two species as adults, many public health workers and vector biologists collecting adults in the field separate these species based on external morphology. This approach is often used rather than examination of dissected male genitalia or polymerase chain reaction (PCR)-based diagnostics due to time or cost constraints. We evaluated the reliability of seven published morphological characters to differentiate adults of these species by comparing blindly scored morphology with PCR-based confirmations. Our study demonstrates that morphological identification of Cx. pipiens is marginal and often not reliable for Cx. restuans. We also examined error rates with molecular-based approaches. DNA samples were contaminated with as little as one leg from another species. We conclude that to fully understand the respective roles of Culex species in the epidemiology of WNV and other pathogens, more attention should be paid to these considerations for accurate species identification.