In an effort to reconstruct the early evolution of animal genes and proteins, there is an increasing focus on basal animal lineages such as sponges, cnidarians, ctenophores and placozoans. Among the basal animals, the starlet sea anemone Nematostella vectensis (phylum Cnidaria) has emerged as a leading laboratory model organism partly because it is well suited to experimental techniques for monitoring and manipulating gene expression. Here we describe protocols adapted for use in Nematostella to characterize the expression of RNAs by in situ hybridization using either chromogenic or fluorescence immunohistochemistry (∼1 week), as well as to characterize protein expression by whole-mount immunofluorescence (∼3 d). We also provide a protocol for labeling cnidocytes (∼3 h), the phylum-specific sensory-effector cell type that performs a variety of functions in cnidarians, including the delivery of their venomous sting.