In order to explore the structural attributes of fish assemblage and its relationship with environmental factors, and to reveal differences in structural characteristics between floating gillnet and benthic gillnet, fishes were caught from Songmushan Reservoir of Guangdong Province using multi-mesh gill nets. The results showed that 17 species, belonging to 4 orders and 6 families, were collected, with the most species-rich order of Cypriniformes (10 species). The index of relative importance (IRI) indicated that Toxabramis houdemeri (IRI:29.66%), Hemiculter leucisculus (18.98%), Oreochromis nilotica (18.46%), Hypophthalmichthys molitrix (14.85%) and Oreochromis mossambica (11.36%) were the dominant species, with T. houdemeri having the highest number per unit effort (NPUE:45.72%) and O. nilotica possessing the largest biomass per unit effort (BPUE:34.60%). No difference in fish composition between seasons was detected by cluster analysis, and no differences in species number, NPUE, and BPUE among seasons were observed. The species number, NPUE, and BPUE did not differed significantly between floating and benthic gillnet. However, a significant difference in numerical composition of fish assemblage between the two types of gillnet was tested, which was responsible for T. houdemeri. The significant higher NPUE for floating gillnets was found than that for benthic ones, but no differences in NPUE between them were detected for the other five fish species. Transparency, total phosphorus, and pH value were the key environmental factors that could be used to explain the temporal and spatial distribution. The results suggested that the low species richness would be related to the small area, low connectivity, invasion of alien fish species, and dominance in inflow river by men-made discharge ditch of this reservoir, and that the floating and benthic gillnets should be both included in sampling procedure for future study in fish community ecology of reservoirs.