We obtained the complete coding genome of an eastern equine encephalitis virus (EEEV) strain, EEEV V105-00210, and the complete genome of a Venezuelan equine encephalitis virus (VEEV) strain, VEEV INH-9813. They were obtained from human cases and are proposed as reference challenge strains for vaccine and therapeutic development in animal models. FOOTNOTES Address correspondence to Gustavo F. Palacios, gustavo.f.palacios.ctr{at}us.army.mil. Citation Yu G-Y, Wiley MR, Kugelman JR, Ladner JT, Beitzel BF, Eccleston LT, Morazzani EM, Glass PJ, Palacios GF. 2015. Complete coding sequences of eastern equine encephalitis virus and Venezuelan equine encephalitis virus strains isolated from human cases. Genome Announc 3(2):e00243-15. doi:10.1128/genomeA.00243-15. Received 19 February 2015. Accepted 4 March 2015. Published 23 April 2015. Copyright © 2015 Yu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.