It is important to study its structure because plankton community changes by the environmental changes in the Antarctic Ocean ecosystem. We here applied the metabarcoding method to analyze the biodiversity of zooplankton in the Indian Ocean of Antarctica, Division 58.4.1 in 2014/15. Compared with the previous method, next generation sequencing (NGS) using Miseq platform produces the large amount of reliable data with relatively low cost. Resulting NGS sequencing two different sized zooplankton populations, 40,376 (56 OTUs and 12 species) and 16,525 (62 OTUs and 16 species) contigs were obtained from large-sized (>1 mm) and small-sized (< 1mm) fractions, respectively. Based on the low numbers of “unknown” OTUs, we were able to know that metabarcoding strategy can be possible in the zooplankton survey only if additional barcode data of small-sized zooplankton or those with soft tissue are supplemented. In both fractions, copepods occupied the highest proportions and Calanoides acutus was the major species among them. Although there were a lot of commonly identified species in both fractions, we were also able to identify several fraction-specific species, which provide several useful ecological information examined zooplanktons. The reproduction of spawning grounds may be estimated by the fish OTS originated from the egg or larvae. From this result, we showed the possibility about the large scale zooplankton survey using the NGS technology for its low cost and time for the analysis.