By using a set of pelagic gillnets with eight mesh sizes, an investigation was made on the spatial distribution of small fishes in submerged macrophyte habitats in a shallow macrophytic lake (Niushan Lake) in the middle reach of Yangtze River in summer, 2005. The fish composition, abundance, and size structure were examined along a biomass gradient of the most dominant submerged macrophyte Potamogeton maackianus. A total of 1124 individuals from 13 fish species were caught during the study period. According to the abundance and occurrence, sharpbelly Hemiculter leucisculus and redfin culter Cultrichthys erythropterus were identified as the two dominant small pelagic fishes in the lake. There existed dome-like relationships between the fish species richness and Shannon diversity index and the submerged macrophyte biomass within its observed range. For the two dominant small fishes, their abundance was significantly positively correlated with macrophyte biomass, and the average sizes of the individuals of H. leucisculus and C. erythropterus were larger in un-vegetated habitat but smaller in heavily vegetated habitats, indicating that the young individuals tended to live in dense submerged macrophyte covers. Other two habitat factors, i. e., water depth and distance to shore, had little effects on the spatial distribution of the two fish species. It was inferred that P. maackianus cover should be the important refuge habitat for the two dominant small-sized fishes in Niushan Lake, and it would be necessary to protect or restore the submerged macrophyte covers including P. maackianus.