<p>To assess the population development of submerged plant species in disturbed lake ecosystems, we need to better understand the genetic diversity and spatial genetic structure at a fine scale, as well as the impact of disturbances on the populations. Caohai Lake, in southwest China, is a suitable natural sampling lake because of its abundance of submerged plants and the intense human disturbance. Three widely distributed species, <i>Potamogeton lucens</i>, <i>Ceratophyllum demersum</i>, and <i>Myriophyllum spicatum</i>, were sampled; the spatial position of each individual was recorded in two-dimensional coordinates; and the species were analyzed genetically using microsatellite markers. Among the species studied, <i>M. spicatum</i> exhibited the highest genetic and clonal diversities. All <i>P. lucens</i> subpopulations but one showed a significant fine-scale spatial genetic structure (FSGS), which may result from the limited gene dispersal. However, <i>M. spicatum</i> and <i>C. demersum</i>, with a relatively large distance of gene dispersal, had no significant FSGS. The FSGS pattern of <i>P. lucens</i> at the dock site with intense boat disturbance was significantly different from that at other sites. Our results imply that the FSGS of submerged plants is affected by many factors including seed dispersal, vegetative reproduction and disturbance from birds and boats. Most subpopulations of the three species had <i>σ</i><Stack> _scx ² </Stack>/<i>σ</i><Stack> _veg ² </Stack> values greater than one, implying that the sexual dispersal contributes more than vegetative dispersal to total gene dispersal. Therefore, it is worth paying attention to the importance of seed dispersal for population development of submerged plants in lake ecosystems.</p>