Abstract The jumbo squid ( Dosidicus gigas ) supports important fisheries, with the maximum landings being recorded in Mexico, Peru and Chile. To evaluate genetic structure and to measure the impact of temporal variation, randomly amplified polymorphic DNA (RAPD) data were generated and analysed from 210 samples from eight eastern Pacific sites and on two sample sets taken from the same location in consecutive years. The temporal variation was shown to have no significant effect on genetic diversity. In addition, a genetic structure was detected which divided the populations into northern and southern locations. There was marginal isolation by distance between populations. Like in other ommastrephids, genetic structure is considered evidence of an adaptive radiation.