We compared two different zooplankton data sets simultaneously obtained at the same place with different mesh-sized nets. Smaller mesh-sized net yielded less diverse zooplankton taxa. However, it was difficult to generalize the relationship between the size of the mesh of the net used and the length of the species list observed. It was not only because the sample sizes obtained by smaller mesh net were relatively smaller due to the clogging problem but also because smaller mesh net usually collected more tiny animals that were difficult to identify at lower taxonomic categories. In terms of abundances, on the other hand, the smaller and the larger mesh-sized nets collected smaller and larger-sized animals more effectively, respectively. The abundances of small sized animals were usually greater than those of large-sized animals by about an order of differences. Due to this different catchability of the nets, the community analyses based on Principal Component Analysis led to different results for the same community.