Venezuelan equine encephalitis viruses (VEEV) are emerging pathogens of medical and veterinary importance circulating in America. Argentina is a country free from epizootic VEEV activity, with circulation of enzootic strains belonging to Rio Negro virus (RNV; VEEV subtype VI) and Pixuna virus (PIXV, VEEV subtype IV). In this work, we aim to report the sequencing and phylogenetic analyses of all Argentinean VEE viruses, including 7 strains previously isolated from mosquitoes in 1980, 5 sequences obtained from rodents in 1991 and 11 sequences amplified from mosquitoes between 2003 and 2005. Two genomic regions, corresponding to the non-structural protein 4 (nsP4) and the protein E3/E2 (PE2) genes were analyzed, but only 8 samples could be amplified in the last one (longer and more variable fragment of 702bp). For both genomic fragments, phylogenetic trees showed the absence of lineages within RNV group, and a close genetic relationship between Argentinean strains and the prototype strain BeAr35645 for PIXV clade. The analysis of nsP4 gene opens the possibility to propose a possible geographic clustering of strains within PIXV group (Argentina and Brazil). Coalescent analysis performed on RNV sequences suggested a common ancestor of 58.3years (with a 95% highest posterior density [HPD] interval of 16.4–345.7) prior to 1991 and inferred a substitution rate of 9.8×10−5substitutions/site/year, slightly lower than other enzootic VEE viruses. These results provide, for the first time, information about genetic features and variability of all VEEVs detected in Argentina, creating a database that will be useful for future detections in our country. This is particularly important for RNV, which has indigenous circulation.