Metagenetic analysis is a recently introduced, taxonomically comprehensive method for characterizing zooplankton communities; however, effects of plankton net characteristics (mesh and opening sizes) on metagenetic data, and biodiversity data in particular, have not been fully evaluated. To this end, we collected zooplankton samples from the subarctic coastal waters off Japan using two plankton nets: 1) Kitahara Quantitative Plankton Net (Kitahara net) with a 0.04-m(2) opening and 100-mu m mesh and 2) North Pacific Standard Plankton Net (Norpac net) with 0.16-m(2) opening and 335-mu m mesh. We then conducted 18S rDNA metagenetic and morphological analyses of the resulting catches. Molecular operational taxonomic units (MOTUs) at 97% similarity revealed higher diversity than did the morphological analysis, especially for morphologically unidentified taxa (e.g., Gastropoda and Polychaeta larvae), suggesting the effectiveness of the metagenetic method for characterizing zooplankton communities. Samples obtained with the Kitahara net produced more sequence reads of non-metazoan taxa, mainly derived from phytoplankton, leading to smaller numbers of available sequence reads for metazoan plankton. Numbers of morphological taxa were higher in the Norpac net samples. However, we expected metagenetic analysis to reveal higher diversity for the Kitahara net, due to larger MOTU numbers from smaller-sized taxa. Small-sized taxa also accounted for a larger proportion of sequence reads in the Kitahara net samples. In contrast, the diversity of large-sized taxa was better represented in the Norpac net sample. Although these differences were expected from the morphological analysis, effects of plankton net characteristics were more clearly reflected by metagenetic analysis than the morphological analysis. (C) 2015 Elsevier B.V. All rights reserved.