Although the effects of a certain seaweed on microbial community structure have been focused, the response of microbial communities to different seaweed cultivation and seasons is poorly understood. To understand microbiome diversity, community structure, interactions and functions with seaweed and seasons, a total of 39 seawater samples in different zones and growth periods during three months were collected from the Neoporphyra haitanensis cultivation zones (P), Gracilaria lemaneiformis-Saccharina japonica mixed cultivation zones (G) and control zones (C).