Abstract Suitable habitat for many temperate freshwater species of salmonids is predicted to dramatically decline, yet many hatcheries still release millions of juvenile salmonids into rivers and lakes annually with little or no post release monitoring. This is, in part, because marking of hatchery reared fish is often not compulsory and currently available marking methods are either costly, cause high mortalities, are inconvenient to apply, or have poor long-term retention rates. To help overcome these limitations, we tested two recently validated stable isotope mass marking methods for Atlantic salmon (larval and egg immersion), to determine if a suitable low cost, easy to apply, fish friendly marking method could be achieved for two of the most widely stocked freshwater salmonids worldwide: brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss. Egg immersion using 1000 μg L−1 of 137Ba and 136Ba over a 2 h period did not create detectable marks in the otoliths of brown or rainbow trout. In contrast, larval immersion using 100 μg L−1 of 137Ba and 136Ba over a 24 h period returned a 100% mark-success rate in the otoliths of brown and rainbow trout at an estimated marking cost of $US 0.004 per fish. Larval immersion marks were clearly definable in the otoliths, with isotope ratios in marked fish 11 times greater than ratios measured in control fish. Furthermore, the process of marking was easy to apply, with