To determine the serotype and genotype of dengue virus (DENV) in Bhutan, we conducted phylogenetic analyses of complete envelope gene sequences. DENV-2 (Cosmopolitan genotype) predominated in 2004, and DENV-3 (genotype III) predominated in 2005-2006; these viruses were imported from India. Primary dengue infections outnumbered secondary infections, suggesting recent emergence.