Shotgun metagenomic sequencing has been one of the indispensable techniques in environmental microbiology by the advancement of high-throughput sequencing technologies. However, limitation of sample volume, low biomass and/or the presence of high concentration of humic substances are issues for application of shotgun metagenomics for deep-sea environments such as bathypelagic to hadal waters, benthic habitats under oligotrophic oceans and subseafloor sediment. Here, we examined applicability of library construction kits based on adaptor ligation technique or tagmentation such as KAPA Hyper Prep Kit, Nextera XT DNA Library Preparation Kit and Ovation SP+ Ultralow Library Systems on shotgun metagenomic library for low amount of environmental DNA (0.1 to 1ng) from abyssal marine sediment, and compared microbial communities from the shotgun metagenomic libraries obtained by the three library construction kits.