Chemical marking of otoliths via immersion in solutions of enriched stable isotopes provides a means of distinctively marking large batches of hatchery-produced fish. Four enriched stable isotopes (barium: 137Ba and 138Ba; strontium: 88Sr; magnesium: 24Mg) were used individually and in combination to determine mark success and the ability to correctly classify 15 unique batch marks in the otoliths of larval Murray cod Maccullochella peelii. Marking with the enriched stable isotopes 137Ba, 138Ba, and 88Sr (individually or in combination) produced clear and distinctive marks (98% mark success) with 93% of fish correctly classified to their respective isotope mark. Despite exposure of the fish to an altered Mg isotope ratio in the water, a corresponding shift in the otoliths was not observed (8% mark success), and many 24Mg-enriched fish were misclassified. Due to the low cost and minimal effects on hatchery protocols, the use of Sr and Ba isotopes to mark hatchery-reared fish at the larval stage has the potential to be a powerful tool in the production and management of a wide range of fish species.