We combined Expansion-Assisted Iterative Fluorescence in situ hybridization (EASI-FISH) with retrograde tracer labeling to reveal the spatial and axonal projection patterns of molecularly defined neuronal types in the central amygdala (CEA). Here, 29 marker-genes were measured with EASI-FISH in 100µm thick brain slices in the mouse CEA, after retrograde tracer labeling in 5 downstream brain targets: the bed nucleus of the stria terminalis (BNST), lateral substantia nigra (lateral SN), periaqueductal gray (PAG), parabrachial nucleus (PBN), and parvocellular reticular formation (PCRt). 'CEA_mFISH_data.csv' contains spot count for all marker genes, axonal projections, spatial locations (z, y, x) and cell body size (area) and shape (solidity), and cell_cluster for each neuron. Each row represents measurement from one neuron. Data collected in six samples from two animals are included here.