Highlands J virus (HJV) is a member of the genus Alphavirus, family Togaviridae. HJV is the sole representative of the western equine encephalitis (WEE) serocomplex found in the eastern United States, and circulates in nature in an apparently identical transmission cycle as eastern equine encephalitis virus (EEEV). North American representatives of the WEE serocomplex [HJV, WEE virus (WEEV), and Fort Morgan virus (FMV)] are believed to be derived from a recombination event involving EEEV and a Sindbis (SIN)-like virus, such that the nonstructural polyprotein, the capsid, and the terminal end of the 3' UTR are derived from EEEV, while the surface glycoproteins (E1 and E2) and small peptides (E3 and 6K) encoded in the subgenomic RNA are derived from the SIN-like virus. In this report, the complete nucleotide sequence of HJV is described, along with a comparative analysis of the HJV nonstructural polyprotein to WEEV and EEEV.