Traditionally, biodiversity has often been estimated on the basis of abundance partly due to the need for complicated measurements of biomass. Here, we conducted robust measurements of the community composition and of the size structure of diatoms in the North Pacific to evaluate the importance of biomass on the biodiversity. We found that the two most useful evenness indices increased in most cases where small species were numerically dominant when calculations were based on biomass compared with those on abundance. Size-abundance spectra of diatoms revealed that numerically dominant small species rarely dominated in terms of biomass. On the other hand, intermediate to large diatom species generally played a dominant role in terms of biomass in diatom community. The results suggest that the size of the dominant species is a crucial factor in determining the role of diatoms in the ecosystem functioning. Because such size variability can also be observed in other organisms, we need to pay attention to the effect of size structures on biodiversity.