Metagenetic approach is rapidly developing method for revealing community structure from bulk environmental samples. Marine planktonic copepods are diverse and abundant groups in the marine pelagic environments, and the metagenetic method using Roche 454 was constructed for copepods. However, Illumina MiSeq, which can produce more than ten times as many sequence reads as Roche 454, has been getting common sequencing platform. Here, we re-evaluated metagenetic method approach for revealing community structure of marine planktonic copepods using Illumina MiSeq. Because Illumina MiSeq can produce much more sequence reads, the developed method would be helpful for monitoring copepod community and dietary study in the future.