In order to develop effective methods on fish sampling at different habitats as well as to test the assumption that collection of fishes by passive gear in specific habitat should ensure at least a time coverage of 24h, both day and night surveys on fish assemblages in seven habitats(i.e., rocky reef, sandy bottom, soft-bottom, hard bottom, artificial reef, cage aquaculture and mussel farms) were carried out in Ma'an archipelago, Shengsi, China, from 16th to 27th of September, 2009, using multi-mesh trammel nets. The species composition, relative abundance and biomass, species richness and diversity, species similarity were compared between two sampling period and among different habitats. Multi-variable statistics such as cluster analysis and non-metric multidimensional scaling (nMDS) were used to explain the fish assemblage patterns from our diel fish collections. A total of 55 species, belonging to 2 classes, 8 orders, 37 families and 50 genera, among which, 28 families and 38 genera at daytime, 34 families and 44 genera at night, were collected from our 24 diel samplings in 12 sites. The diel shift patterns of habitat use by fishes varied with their eco-types, especially with their habitation on certain water levels. More ground fishes, such as Sebastiscus marmoratus and Plotosus anguillaris, were collected at night in hard-substrate habitats (i.e. rocky reef and artificial reef habitat) than daytime. The diel variations of near-ground fish assemblages varied at different habitats. Some of them had a much higher occurrence (e.g. Stephanolepis cirrhifer ) during daytime while others(e.g. Pagrus major) appeared frequently at night. Pelagic fishes such as Thryssa kammalensis were mostly collected during daytime in artificial habitats. In general, a much higher abundance catch rate (ACR) was found in artificial habitats (AHs) during daytime than it was at night. However, no significant diel variations were found in natural habitats (NHs) for both ACR and biomass catch rate. Only few species, including Larimichthys polyactis and Thryssa kammalensis, were observed with significant diel variations. No significant differences were found in species richness and diversity between daytime and night both in AHs and NHs. Significant changes of fish species were observed due to low species similarity between day and night. Three patterns of fish assemblages can be described, including the dominance of night-tendency fishes such as Sebastiscus marmoratus and Plotosus anguillaris at hard-bottom habitats, the dominance of day-tendency species such as Stephanolepis cirrhifer and Microcanthus strigatus at hard-bottom habitats, and high abundance of Sciaenidae at soft-bottom habitats. Based on the results of the present study, it is recommended that the time duration of any surveys on fish assemblages in coastal areas shall last more than 24h.