Invasive species are one of the greatest threats to global biodiversity and ecosystem health, and population genetics provides promising tools for understanding the evolutionary process of successful invaders. The well-documented introduction of the red lionfish (Pterois volitans) to the western Atlantic, Gulf of Mexico and Caribbean has decimated native fauna due to the invader’s voracious predation and growth rate. We tested whether our samples were within the region of the source of invasion into the Atlantic and Caribbean and investigated whether hybridization in the native or introduced range was responsible for the success of this invasive species. We used a reduced representation sequencing method to generate over 50,000 single nucleotide polymorphisms and sequence data from two mitochondrial DNA genes to analyze the population patterns. We found one location in the southeastern Pacific that was genetically similar to one location the southwestern Atlantic and evidence of the subsequent spread south to the Gulf of Mexico and the Caribbean, which supports previous findings. Within the native range, we found genetic divergences commensurate with distinct species and evidence of hybridization. We found limited structure within the introduced range and no evidence of Pterois miles or hybrids within this range. Finally, we found signatures of selection between the native and introduced range that may be a result of the introduction. Overall, this study of the red lionfish showed the pattern of introduction and suggested a deeper sampling of genomic data from individuals within the native range may reveal hybridization between species as the source of the aggressive invasion.