The starlet sea anemone Nematostella vectensis is an emerging model organism for developmental and evolutionary biology. Due to the availability of genome data and its amenability to genetic manipulation Nematostella serves as a source for comparative molecular and phylogenetic studies. Despite this fact, the characterization of the nematocyst inventory and of nematocyst-specific genes is still fragmentary and sometimes misleading in this cnidarian species. Here, we present a thorough qualitative and quantitative analysis of nematocysts in Nematostella vectensis. In addition, we have cloned major nematocyst components, Nematostella minicollagens 1, 3 and 4, and show their expression patterns by in situ hybridization and immunocytochemistry using specific antibodies. Our data provides tools and insights for further studies on nematocyst morphogenesis in Nematostella and comparative evolution in cnidarians.