Molecular work on “non-traditional” organisms is limited by a lack of specific antibodies and probes for mapping expression of proteins and genes. Hybridization Chain Reaction (HCR) and RNA-seq make reliable, large-scale mapping of neurons more accessible by expanding the pool of potential gene products that can be labeled for almost any animal. We have introduced the nudibranch Berghia stephanieae as a new species for neuroscience research because it has a small brain that can be mapped in its entirety. Here, we used both traditional immunohistochemistry (IHC) and HCR to map the expression of neurotransmitter-related genes to neurons in the Berghia brain. We reproducibly labeled populations of neurons positive for 9 genes: serotonin, small cardioactive peptide, FMRFamide, conopressin, egg-laying hormone, choline acetyltransferase, tyrosine hydroxylase, APGWamide and GABA. Some genes, such as egg-laying hormone, conopressin and tyrosine hydroxylase, the synthetic enzyme for catecholamines, were expressed in only a small and discrete set of neurons. Others, such as choline acetyltransferase, the synthetic enzyme for acetylcholine, were widely expressed. HCR is a fluorescent technique, allowing us to simultaneously label up to 5 genes. We have also combined HCR with IHC in the same sample. Using these techniques we found co-expression of neuropeptides with each other, but other neurotransmitter-associated genes did not overlap in expression. HCR enables broader molecular studies of unorthodox animals and comparisons of gene expression, neurons and brains across the animal phylogeny.