Lake Bourget (4400 ha), located in France, is a deep peri-alpine lake. In the middle of the XX century, populations of whitefish (Coregonus lavaretus) with a littoral spawning (<10m) and of Arctic charr (Salvelinus alpinus) with a deep spawning (40-80 m) collapsed in relation with the eutrophication, but without totally disappearing. Important environmental measures provoked reoligotrophication, P dropping from 120 to 25 μg/L between the initial phase and the beginning of final phase of reoligotrophication. A programme of stocking with the two species was undertook by managers, starting in the middle of the eighteen’s and using local spawners to produce F1 alevins. Thanks to original large scale marking campaigns of small fishes, the present work evaluates the respective contribution of stocking and natural recruitment in the catches during the reoligotrophication process. Some recapture rates were also evaluated. In the initial phase of reoligotrophication , in the eighteens –beginning of the nineteens the stocking with fed alevins have had a very important contribution (88-91% at the dominant 3+ age) allowing to avoid the disappearance and even permitting the rehabilitation of the populations and their associated fisheries (professional, sportive and even spawning stocks). Those results showed that some limitant factors at precocious stages were acting before the stage of fed alevins (presummerlings for whitefish and summerlings for Arctic charr). In the beginning of the final stage of reoligotrophication, the situation and the dymamic of the evolution of catches was quite different for the two species:For the whitefish, the catches strongly increase during reoligotrophication. The contribution of stockings (with 100-320 000 just-fed 14-18mm alevins) is small, near 10%, but however the recapture rates by the professional fishery are good (2,3-7,8 kg/1000 just-fed alevins). The study demonstrates a strong expansion of the functionality of natural recruitment of the population of whitefish. For the Artic charr, the contribution of stocking is always dominant (80-90%) in the catches by the fisheries. On the contrary the recapture rates have decreased during reoligotrophication, from 23-56 to 12-18 kg/1000 summerlings. On the contrary to the whitefish, there is no recovery of an efficient natural recruitment for the Arctic charr. These differential evolutions between the two species during reoligotrophication are discussed using comparative ecology. Practically, in a lake with both natural and artificial recruitment, the present study demonstrated that mass marking campaigns are very useful to evaluate the evolution of the two components of recruitment both in catches by fisheries and at spawner stage.