To examine the specific features of trench communities, spatial changes in the assemblages of harpacticoids were investigated at the family level around the Ryukyu Trench (the Ryukyu region) and Kuril Trench (the Kuril region). In the Ryukyu region, there were high average dissimilarities in the harpacticoid assemblages among the trench, trench slope and abyssal plain, indicating that the assemblage structures differ substantially between these topographic settings at the family level. Conversely, in the Kuril region, the average dissimilarities in harpacticoid assemblages between the trench and the trench slope and between the trench and the abyssal plain were lower than that between the slope and the abyssal plain. This result suggests that the hadal assemblage is a transition zone between the slope and the abyssal plain in this region. In addition, the analyses indicate that the composition of harpacticoid assemblages is influenced by the quantity of organic matter in the Ryukyu region, while sediment properties play a key role in the Kuril region. Comparisons of the assemblages between the two regions, however, revealed that the average dissimilarities between the trenches and between the abyssal plains were higher than that between the adjacent slopes. This result suggests that interchange among regions is difficult for deep-sea benthic animals, including harpacticoid copepods, likely due to the presence of physical barriers around trenches.