Cylindrospermopsis raciborskii is a toxic cyanobacterium with an invasive nature. The species is found in all the main continents but its origin and dispersal routes on a worldwide perspective remain yet mostly unknown. In this study, 27 isolates of C. raciborskii gathered worldwide have been used for an in-deep phylogenetic analyses with a concatenated system of three genetic markers (16 rRNA, 16S-23S ITS larger subunit, and RNA polymerase rpoC1) comprehending 3,188 bp. Our results provide support for an origin of C. raciborskii in the American continent. Dispersal routes included afterward a spread into the African continent and then Asia and Australia, being Europe the last continent to be colonized by this species. Our phylogenetic inferences suggest that C. raciborskii seem to have a well-defined dispersal behavior with a well-established population structure around the world.