Aedes triseriatus is the primary vector of LaCrosse (LAC) virus, which can cause encephalitis, especially in young children. Aedes hendersoni, a sibling species of Ae. triseriatus, has a salivary gland barrier to LAC virus and, therefore, is not considered a vector of this virus. Adults of Ae. triseriatus are morphologically indistinguishable from those of Ae. hendersoni, and the two species are sympatric in the eastern United States. A definitive method of identifying field specimens is an important part of any disease surveillance program, particularly in the case of LAC virus. This study identifies restriction enzymes that produce species-specific restriction fragment length polymorphisms (RFLPs) from amplified ribosomal (r) DNA. In addition, sequences of the internal transcribed spacers 1 and 2 and the 5.8S regions of the rDNA were used to confirm the RFLP patterns. This study is the first to compare nucleotide sequences from Ae. triseriatus and Ae. hendersoni.