The amygdala is a brain region primarily associated with emotional response. For example, fear learning and memory are known to activate neurons in the amygdala, which induce gene expression to strengthen the formation of stable engrams. Single-cell transcriptomics can provide insights into behavior-associated cell state changes. Here we present a detailed cell-type taxonomy of the adult mouse amygdala during fear learning and memory consolidation. We perform single-cell RNA sequencing on naïve and fear-conditioned mice, identify 130 neuronal cell types and validate their spatial distributions. We found that only a subset of all neuronal types is transcriptionally responsive to fear learning and memory retrieval. Within the responsive populations, activated engram cells upregulate activity-response genes and coordinate the expression of genes associated with neurite outgrowth, synaptic signaling, plasticity and development. We identify known and previously undescribed neuronal populations and candidate genes responsive to fear learning. Our molecular atlas may be used to generate hypotheses to unveil the neuron types, neural circuits and genes regulating the emotional component of learning and memory.