Thirteen asexually reproducing clones of Enteromorpha linza were found in samples collected from March to September 1982 in Long Island Sound, USA, based on variation at five enzyme loci. Significant differences in the relative frequency of each clone were observed among samples from 16 localities. There was a tendency for localities at the eastern end of the Sound to form a group genetically differentiated from localities at the western end, but in general there was no strong relationship between geographic distance and genetic distance. Areas separated by only a few hundred meters were genetically differentiated, despite the presence of a dispersing spore stage in this species. Samples from areas of low salinity were genetically similar but distinct from adjacent high salinity areas. One clone restricted to high salinity localities and one associated with low salinity localities were tested for growth under high and low salinity conditions in the laboratory. The clone from the high salinity habitat grew more slowly under low salinity conditions. However, there was no evidence for a detrimental effect of high salinity on the low salinity associated clone. Additional environmental factors, as well as biological factors such as limited recruitment and competitive interactions among clones, may also be important determinants of genetic differentiation among populations of E. linza. Temporal shifts in clone frequency were observed within some localities and may be due to seasonal-dependent regeneration from microscopic holdfasts for different clones or a seasonal recruitment of new clones from other areas. The pattern of differentiation among populations of E. linza in Long Island Sound appears to be maintained by factors operating on a microgeographic scale.