Signatures of trace elements and isotopes in the parts of hard structures formed in the early ontogenetic stages can be used as potential natural tags of adult cephalopods to trace their origins. The Jumbo flying squid, Dosidicus gigas, is widely distributed in the eastern Pacific Ocean. Fourteen detected elemental signatures (7Li, 23Na, 24Mg, 39K, 43Ca 55Mn, 59Co, 60Ni, 63Cu, 66Zn, 88Sr, 137Ba, 208Pb and 238U) were determined in the nuclear zone (N), representing the embryonic stage, and the postnuclear zone (PN), representing the paralarval stage of statoliths for adult D. gigas collected off the Costa Rican, Peruvian and Chilean Exclusive Economic Zones (EEZs) using laser ablation inductively coupled plasma mass spectrometry (LA‐ICP‐MS). All measured signatures were significantly different between embryonic and paralarval statoliths, except for Sr, Ba and Pb. Over the three regions, a significant difference was found for Na and Ba within embryonic statoliths and Zn and Ba within paralarval statoliths. A high Ba/Ca ratio in statoliths obtained from Costa Rica was because of the prevalence of strong upwelling in the area. Elemental signatures, especially Ba/Ca, in early ontogenetic statoliths could be used as a proxy for distinguishing different geographical groups and identifying natal origins. However, elemental signatures in embryonic statoliths tended to be a better natural tag than those in paralarval statoliths indicating that paralarvae with the same origin had distinct dispersal pathways. Additionally, stepwise discriminant analysis (SDA) showed there were at least two migration‐based groups: ‘northern’ and ‘southern’ in the eastern Pacific Ocean. Overall, the derived results can improve our knowledge of the population structure, connectivity and life history of D. gigas.