The ecological environment determines the evolutionary process allowing specialized morphs to emerge in sympatry, but the drivers behind this process are not yet well understood. The parallel evolution among lacustrine fishes implies the existence of basic and universal drivers of sympatric diversification. We assumed that these might be dyschronic annual oscillations of food resource abundance for different niches. A tiny ecosystem inhabited by two reproductively isolated salmonid morphs was chosen as the simplest model to test this hypothesis using ecological and modelling approaches. We found that the ontogenetic timing of the morphs is synchronized with diametrically shifted annual resource maxima in the pelagic and benthic zones. Using food niche data and long-term environmental modelling, we confirm that these shifts are driven by environmental factors with high inter-annual repeatability making them key drivers of parallel evolution in lacustrine fishes. These results allow us to explain how the diversification process works in the large number of northern ecosystems with four seasonal climates. Furthermore, our findings give the direct clues to embed the natural data into Levin-type models for future explanations and predictions of northern fish diversifications in natural and artificial waterbodies.