Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes Chikungunya fever. CHIKV entered Mexico through the state of Chiapas in October 2014. To fully understand the Chikungunya fever outbreak that occurred in southern Chiapas during 2015, we evaluated 22 PCR-confirmed CHIKV-positive patients, identified CHIKV genetic variability, reconstructed viral dispersal, and assessed possible viral mutations. Viruses were isolated and , , and genes were sequenced. We applied phylogenetic and phylogeographic approaches, modeled mutations, and estimated selective pressure. Different CHIKV strains circulated in Chiapas during summer 2015. Three isolates grouped themselves in a well-supported clade. Estimates show that the outbreak started in Ciudad Hidalgo and posteriorly dispersed towards Tapachula and neighboring municipalities. We found six non-synonymous mutations in our isolates. Two mutations occurred in one isolate and the remaining mutations occurred in single isolates. Mutations E2 T116I and E2 K221R changed the protein surface in contact with the host cell receptors. We could not find positive selected sites in our CHIKV sequences from southern Chiapas. This is the first viral phylogeographic reconstruction in Mexico characterizing the CHIKV outbreak in southern Chiapas.