Microbial community varies depending on habitat types, but it is still unclear how the microbial community of each habitat communicates. In dairy farms, cows take in microbes from the environment, e.g., eating grasses, and their dung is fermented and supplied to soils with the associated microbes. Hence, we expected the microbes to cycle within the farm, which makes unique microbes to each farm, and the communities in different habitats on a farm might have specific networks. Here, we collected grasses, dungs, manures, and soils, and wiped walls, as different habitats of microbes, in 15 dairy farms of Hokkaido, then analyzed the bacterial community compositions. Bacteria common in all the habitats (wall, grass, dung, manure, and soil) were limited, but many bacteria appeared in >2 habitats. These frequent bacteria and the community structure were different among the farms. Besides, the bacterial community composition in one habitat affected that of another habitat (e.g., wall affected dung, manure affected soil), and in some farms, the network analysis suggested connections between bacteria from different habitats. Thus, some unique bacteria to each farm partly moved inside the farms, and the bacterial community in a habitat had specific connections with that of other habitats.