The mosquito-borne chikungunya virus, an alphavirus of the Togaviridae family, is responsible for acute polyarthralgia epidemics. Here, we report the complete genome sequences of two chikungunya virus strains, InDRE04 and InDRE51, identified in the Mexican states of Jalisco and Chiapas in 2014. Phylogenetic analysis showed that both strains belong to the Asian genotype. FOOTNOTES Address correspondence to José Alberto Díaz-Quiñonez, alberto.diaz{at}salud.gob.mx. Citation Díaz-Quiñonez JA, Ortiz-Alcántara J, Fragoso-Fonseca DE, Garcés-Ayala F, Escobar-Escamilla N, Vázquez-Pichardo M, Núñez-León A, Torres-Rodríguez MDLL, Torres-Longoria B, López-Martínez I, Ruíz-Matus C, Kuri-Morales P, Ramírez-González JE. 2015. Complete genome sequences of chikungunya virus strains isolated in Mexico: first detection of imported and autochthonous cases. Genome Announc 3(3):e00300-15. doi:10.1128/genomeA.00300-15. Received 27 February 2015. Accepted 23 March 2015. Published 7 May 2015. Copyright © 2015 Díaz-Quiñonez et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.