A fundamental goal of ecology is to identify rules that reflect species interactions; however, empiricalexamples of assembly rules for fish species in bays are limited. Analyzing the relative roles of niche separationand habitat filtering is a good way to elucidate the species mechanism. We investigated the mechanisms of howspecies in fish assemblages within bays coexist, using Meizhou Bay as a case study with null models. C-score,number of species checkerboard pairs, and the standard effect size index based on binary data were not differentbetween the observed and simulated values. Similarly, the Pianka and Czechanowski niche overlap index also indicatedno difference between observed and simulated values, according to the abundance matrix, suggesting thatfish assemblages within this system have a random pattern that is structured simultaneously by niche-partitioningand niche-filtering effects. Therefore, preservation and conservation strategies must include habitat restoration,maintaining the connection between the bay and adjacent area, and increasing population size. These results willbe useful for developing local biodiversity management and conservation strategies.