Sex allocation is the most successful application of evolutionary game theory. This theory has usually been applied to multicellular organisms; however, conditional sex allocation in unicellular organisms is a completely unexplored field. Observations at the cellular level are indispensable for an understanding of the phenotypic sex allocation strategy among individuals within clonal unicellular organisms. The diatom Cyclotella meneghiniana, in which the sexes are generated from vegetative clonal cells, is suitable for investigating effects of phenotypic plasticity on sex allocation while excluding genetic differences. We designed a microfluidic system that allowed us to trace the fate of individual cells. Sex allocation by individual mother cells was affected by cell lineage, cell size, and cell density. Sibling cell pairs tended to differentiate into the same fates (split sex ratio). We found a significant negative correlation between size of the mother cell and sex ratio of the two sibling cells. The male-biased sex ratio declined with higher local cell population density, supporting the fertility insurance hypothesis. Our results characterize multiple factors that affect the phenotypic single cell-level sex allocation strategy. Sex allocation in diatoms may provide a model system for testing evolutionary game theory in unicellular organisms.