Levels of genetic diversity can be used to determine haplotype frequency, population size and patterns of invasive species distribution. In this study, we sought to investigate the genetic structure of the invasive marine mussel Mytella charruana and compare variation from invasive populations with variation found within three native populations. Invaded areas in the USA (Florida, Georgia); native areas in Ecuador, Colombia and Brazil. We sequenced 722 bp of the mitochondrial COI gene from 83 M. charruana samples from four invasive populations (USA) and 71 samples from two natural populations (Ecuador, Columbia). In addition, we sequenced 31 individuals of a congeneric species, Mytella guyanensis, from Salvador, Brazil. We constructed the phylogenetic relationship among all haplotypes and compared diversity measures among all populations. We found significantly higher levels of nucleotide diversity in invasive populations than in native populations, although the number of haplotypes was greater in the native populations. Moreover, mismatch distribution analyses resulted in a pattern indicative of population admixture for the invasive populations. Conversely, mismatch distributions of native populations resulted in a pattern indicative of populations in static equilibrium. Our data present compelling evidence that the M. charruana invasion resulted from admixture of at least two populations, which combined to form higher levels of genetic diversity in invasive populations. Moreover, our data suggest that one of these populations originated from the Caribbean coast of South America. Overall, this study provides an analysis of genetic diversity within invasive populations and explores how that diversity may be influenced by the genetic structure of native populations and how mass dispersal may lead to invasion success.