Imaging is a critical tool in neuroscience, and our understanding of the structure and function of sea urchin nervous systems owes much to this approach. In particular, studies of neural development have been facilitated by methods that enable the accurate identification of specific types of neurons. Here we describe methods that have been successfully employed to study neural development in sea urchin embryos. Altering gene expression in part of an embryo is facilitated by injection of reagents into individual blastomeres, which enables studies of cell autonomous effects and single embryo rescue experiments. The simultaneous localization of an in situ RNA hybridization probe and a cell type specific antigen has enabled studies of gene expression in specific types of neurons. Fixatives and antibodies can be capricious; thus, we provide data on preservation of antigens with commonly used fixatives and buffers.