Micro X-ray fluorescence (µ-XRF) analysis of otoliths was evaluated as a method to estimate the proportion of stocked one-summer-old whitefish Coregonus lavaretus L. in catches of adult fish (n = 20) ascending the River Kemijoki to spawn. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) analysis was applied as control. Polished otoliths were scanned with µ-XRF to obtain strontium maps that were used to infer visually the provenance of the whitefish. Thirteen of the fish showed signs of being stocked as one-summer-old fingerlings. LA-ICP-MS was applied to determine the elemental composition in a spot outside the core of the otolith. The results were largely consistent with the visual inspection of the µ-XRF mapped otoliths. In conclusion, µ-XRF mapping successfully identified whitefish stocked as one-summer-old fingerlings. The vast majority of whitefish returning to the River Kemijoki to spawn were stocked fish.