A total of 44 wild jaguarundis were sampled throughout Mexico, Guatemala, Costa Rica, Colombia, Venezuela, Ecuador, Peru, Bolivia and Brazil and sequenced for three mitochondrial genes (ATP8, 16S rRNA, NADH5). This is the first molecular population genetics and phylogenetic study of this species and the most relevant results were as follows: 1-The gene diversity levels for the jaguarundi at the three mitochondrial genes sequenced were very elevated as it was found for other Neotropical wild cats such as the jaguar, ocelot, margay and the Pampas cat; 2-The levels of gene heterogeneity among putative subspecies or among countries was extremely small, although this species has a broad distribution from southern USA to Argentina; 3-Additionally, the phylogenetics trees (genetic distances, maximum likelihood, maximum parsimony and Bayesian) showed that no molecular subspecies were defined in contradiction with the morphological classifications of Allen (1919), Cabrera (1957) and de Oliveira (1998); 4-Bayesian and network procedures showed that the first haplotype divergence process in the jaguarundi began around 2.0-1.6 MYA, with a second haplotype divergence event around 1.1-0.8 MYA, followed by other haplotype splits around 0.75-0.5 MYA, 0.34-0.32 MYA, and 0.16-0.11 MYA as well as many haplotype divergence events in the last