The randomly amplified polymorphic DNA (RAPD) assay was used to identify genetic polymorphisms in three clonal populations of the freshwater bryozoan, Cristatella mucedo, a species with few useful biochemical genetic markers. Of the 19 decamer oligonucleotide primers screened, 13 gave clear, reproducible RAPD profiles. Clonal population structure was evident, and one clone was dominant at each site. Cluster analysis grouped populations from more distant localities separately (Thames Valley and Norfolk), whereas populations from the Thames Valley clustered together. However, even at the regional scale a high degree of relatedness pertained. This work is one of the first RAPD studies of natural populations, and demonstrates the suitability of the technique for examining population structure and geographic variation in clonal taxa.