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This dataset presents the fingerprinting scores of 160 different clonal isolates of the freshwater diatom Asterionella formosa based on amplified fragment length polymorphism (AFLP). As Asterionella colonies consist of uniclonal cells only, isolating single colonies is a simple way to achieve uniclonal cultures. Culture establishment from isolated colonies was fairly unbiased with a larger than 95% success rate. The AFLP analysis was performed by Keygene® (Wageningen, The Netherlands) using the same four EcoRI/Msel AFLP primer combinations as reported in De Bruin et al (2004), a) Eco+GA & Mse+AT, b) Eco+GA & Mse+CC, c) Eco+GA & Mse+CG, d) Eco+GC & Mse+AC. In the AFLP analysis each locus was treated as a separate character and scored for presence or absence, yielding a binary data matrix for each early and late bloom subset of genotypes separately.