Abstract The potential to discriminate between wild and hatchery trout [Salmo trutta f. fario L. and Oncorhynchus mykiss (Walbaum)] by chronological microchemical patterns of different otolith regions was tested. Central and rim regions of otoliths were analysed for life stage specific elemental patterns of strontium (Sr), sodium (Na) and calcium (Ca) as well as of 87Sr/86Sr ratios using laser ablation inductively coupled plasma mass spectrometry (LA‐ICP‐MS). Classification to life stage specific habitats was achieved with 100% accuracy by 88Sr/43Ca, 23Na/43Ca and 87Sr/86Sr ratios resulting in a discrimination of hatchery fish from wild fish. 87Sr/86Sr ratios and Sr concentration in otoliths were positively correlated with the ratio and amount in the water. Na content in otoliths did not directly reflect the concentration in the water, although the 23Na/43Ca ratio in otoliths contributed to the discrimination. Clear differences in otolith chemistry were found for fish experiencing different geological units or a groundwater‐fed environment in a hatchery. Natural chronological microchemical patterns in otoliths proved to be a valuable tool for discriminating wild and hatchery fish without the necessity to use marking methods. LA‐ICP‐MS is well suited for this application because of its limited need for sample preparation, its potentially high sample throughput and the possibility of simultaneous measurement of multiple elemental and isotopic fingerprints.