Summary: Pyrosequencing technologies are frequently used for sequencing the 16S rRNA marker gene for profiling microbial communities. Clustering of the produced reads is an important but time-consuming task. We present DySC, a new tool based on the greedy clustering approach which uses a dynamic seeding strategy. Evaluations based on the normalized mutual information criterion shows that DySC produces higher quality clusters than UCLUST and CD-Hit at a comparable runtime.