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Using mathematical modeling methods, the work investigates possible existence of a phytoflagellate population in the ecosystem of a stratified lake (Lake Shira, Khakasia, Russia). Until this study was carried out, no phytoflagellate population had been detected in the lake, although there had been indirect evidence of the possible presence of a cryptomonad population in this water body. To answer the question if this population may be present in this water body, as the first step of investigation, a mathematical model was developed describing the microorganism biomass dynamics and phytoflagellate relationship with the lake food web. The calculations showed that cryptophytic algae were abundant in the water column layers above the lake chemocline at the beginning of summer but showed low biomass concentrations during other periods of time. In the summer following the construction of the model, samples were collected from Lake Shira, as the next step of the study. A cryptophytic algae population was found in the water column, and the pattern of its distribution in the ecosystem was similar to that predicted by the model. In addition to that, we studied theoretically possible reasons for the early summer development of the population in the deep water layers and found that it was the result of the mixotrophic feeding strategy of cryptomonads and trophic interactions in the food web. The study shows that preliminary modeling of the locational and temporal distribution of populations whose presence in the ecosystem is only suggested by indirect evidence may be useful as a tool for searching for the species in natural ecosystems and as an approach enabling a more accurate description of the food web structure of a water body.