Members of the New World mosquito subgenus Melanoconion of the genus Culex are important vectors of many alphaviruses including eastern and Venezuelan equine encephalitis viruses (VEEV). We investigated the phylogenetic relationships among nine putative species of the Vomerifer and Pedroi Groups of the Neotropical Spissipes Section by sequencing the internal transcribed spacer 2 (ITS-2) region of ribosomal DNA and using phylogenetic analyses. Results demonstrated that, within the Spissipes Section, the Vomerifer and Pedroi Groups are monophyletic sister groups. The clade comprised by Culex adamesi and Culex ribeirensis showed a sister group relationship to the group consisting of Culex pedroi sequences. The monophyly of the Vomerifer Group corroborated previous suggestions that it is a natural group. However, our topology showed that there are two well-supported, divergent groups within a major clade consisting of Cx. pedroi sequences, suggesting the possibility of a cryptic Cx. pedroi–like species. This finding could have important epidemiological implications for VEEV transmission in Central and South America.