The complete nucleotide sequences of the envelope gene of 62 geographic isolates of St. Louis encephalitis (SLE) virus were determined. Phylogenetic analyses of the sequences, conducted using both maximum parsimony and neighbor-joining methods, included four other members of the Japanese encephalitis serogroup. The results indicated that the SLE isolates formed a monophyletic group in which isolates generally clustered according to geographic origin. Isolates from Panama and South America predominantly formed two large groupings, while isolates from the U.S. formed two other major groups. Several South and Central American strains were more closely related to strains isolated in the U.S., e.g., one isolate from Mexico and Panama, each, were closely related to two Tampa Bay, Florida, isolates, and an isolate, from Brazil was closely related to three isolates from Texas. The U.S. isolates also were not strictly grouped according to geographic source, e.g., some California isolates were closely related to Texas or midwestern isolates, and a Florida isolate was closely related to three isolates from Maryland. The results of the phylogenetic analyses indicated that SLE virus is predominantly maintained locally, but has been transported occasionally between areas, both within and outside the U.S.