Sea cucumbers are benthic deposit-feeders making a significant contribution to the maintenance of marine benthic ecosystems. Bioturbation, sediment cleaning, nutrient recycling, and biodiversity enhancements are well documented key ecological functions performed by the animals. However, the contributions of their gut microbiomes to these ecological functions are largely unknown due to a lack of knowledge on the annual dynamics of microbial communities and their functions. Here, we performed spatiotemporally-broad meta16S rRNA analyses using 111 samples from feces and sediments collected from major northern and southern sea cucumber habitats in Japan.