The lionfish (Pterois volitans), has become an abundant alien species along the southeast coast of the United States of America and in Caribbean coastal waters. Although, they represent a major concern in conservation, no studies have yet assessed their population ecology and genetic structure simultaneously. We collected 227 lionfish from 24 sites around Puerto Rico to investigate, the length distribution, length-weight relationships, relative condition factor, and mitochondrial DNA (mtDNA) genetic diversity. The total length distribution ranged between 37 and 349 mm with a single peak between 130 and 149 mm. Our analysis indicated isometric growth for mature individuals and a positive allometric growth for immature lionfishes. These results suggest a different allocation of resources, most likely reproduction for mature individuals and somatic growth for the immature lionfish. The relative condition factor (KN) was similar for immature and mature individuals. Genetic analyses indicated that P. volitans is the only lionfish species present in Puerto Rico, and that its origin was likely dispersal from the epicenter of introduction off the coast of Florida. Interestingly, only four of the nine mtDNA haplotypes identified in the Atlantic were observed in the Puerto Rican population. A fine-scale population genetic analysis suggested a significantly different population structure between the west and south coasts. Finally, our data suggests a second founder effect, but with a reduction of haplotype diversity. © 2014 The Author(s).