Measurements of cell density, nutrient concentration and genotype composition in a long term experiment (91 days) with the marine phytoplankton species Chaetoceros affinis and Emiliania huxleyi, each consisting of nine genotypes. Cultivation of species was done separately in mono-cultures and together in mix-cultures at three different nutrient regimes (10N:1P, 20N:1P, and 30N:1P) with increasing nitrate concentration in a semi-continuous batch cycle system. Transfer of part of the cells into bottles with new nutrients every 7 days at fixed batch cycle length and after 7,4, and 10 days in a recurring fashion at variable batch cycle length. With the information about the genotype abundance we assessed how intraspecific diversity is maintained in response to species competition and nutrient fluctuations. Individual trait measurements for growth, nutrient uptake, and cell volume of the genotypes at seven nitrate levels in a 4-day experiment allowed us to connect traits to the genotype sorting of the long term experiment.