Spores of Tetrachaetum elegans were isolated in early autumn from submerged leaves which were randomly collected at a single site from a small stream in southwestern France. In order to investigate potential substrate preferences, spores were sampled in four leaves from seven different plant genera. A total of 96 monosporic isolates were screened for genetic variation in RAPD patterns using nine different primers. Fifty-two fragments were identified and used for calculation of similarity coefficients. A large number of fragments were shared across all isolates, suggesting that the population was genetically homogeneous. The combination of 11 polymorphic fragments contributed to the delineation of 13 RAPD types. Colonization of a single leaf by multiple genotypes was frequently encountered. Fungal genetic assemblages differed between plant genera. Variations in the frequency of occurrence of the various genotypes are discussed in terms of ecological strategies and in reference to previous work at the community level. We suggested two hypotheses: first, substrate preferences are found among aquatic hyphomycete genotypes, and secondly, sequential occupation by distinctive populations may result in different assortments of genotypes on leaf litters of different plants at any given time of sampling.