Key points Carotid body (CB) glomus cells mediate acute oxygen sensing and the initiation of the hypoxic ventilatory response, yet the gene expression profile of these cells is not available. We demonstrate that the single cell RNA‐Seq method is a powerful tool for identifying highly expressed genes in CB glomus cells. Our single cell RNA‐Seq results characterized novel CB glomus cell genes, including members of the G protein‐coupled receptor signalling pathway, ion channels and atypical mitochondrial electron transport chain subunits. A heterologous cell‐based screening identified acetate (which is known to affect CB glomus cell activity) as an agonist for the most highly abundant G protein‐coupled receptor (Olfr78) in CB glomus cells. These data established the first transcriptome profile of CB glomus cells, highlighting genes with potential implications in CB chemosensory function. Abstract The carotid body (CB) is a major arterial chemoreceptor containing glomus cells whose activities are regulated by changes in arterial blood content, including oxygen. Despite significant advancements in the characterization of their physiological properties, our understanding of the underlying molecular machinery and signalling pathway in CB glomus cells is still limited. To overcome this, we employed the single cell RNA­Seq method by performing next‐generation sequencing on single glomus cell­derived cDNAs to eliminate contamination of genes derived from other cell types present in the CB. Using this method, we identified a set of genes abundantly expressed in glomus cells, which contained novel glomus cell‐specific genes. Transcriptome and subsequent in situ hybridization and immunohistochemistry analyses identified abundant G protein‐coupled receptor signalling pathway components and various types of ion channels, as well as members of the hypoxia‐inducible factors pathway. A short‐chain fatty acid olfactory receptor Olfr78, recently implicated in CB function, was the most abundant G protein‐coupled receptor. Two atypical mitochondrial electron transport chain subunits (Ndufa4l2 and Cox4i2) were among the most specifically expressed genes in CB glomus cells, highlighting their potential roles in mitochondria‐mediated oxygen sensing. The wealth of information provided by the present study offers a valuable foundation for identifying molecules functioning in the CB.