The classification of the ecological niche and the grouping of species into generalists and specialists are established ecological concepts. In this study, we compare two methods for the calculation of the realized ecological niche from long-term species data. As the first method, we present a new approach to reconstruct the realized niche not in terms of abundance but via a measure of fitness (optimal niche), which we call the Optimal Niche Estimate (ONE). The second method, the outlying mean index (OMI) analysis, is performed with abundance data for calculating the ecological niche. We demonstrate and discuss differences between methods by applying them to time series of three phytoplankton species from the Helgoland Roads long-term data set: Ceratium fusus, Odontella regia, and Paralia sulcata.