Neurons in the dorsal motor nucleus of the vagus (DMV) and nucleus ambiguus pars compacta (NAc) innervate the subdiaphragmatic oesophagus in rodents but little is known about the central circuitry that controls the activity of these vagal motor neurons. We assessed the monoamine innervation of these two groups of esophageal motor neurons with immunohistochemistry, conventional retrograde tracing and anterograde tracing using lentiviral vectors that drive GFP expression in either catecholamine or 5‐HT neurons. Close appositions from axons immunoreactive for 5‐HT or catecholamine synthetic enzymes (tyrosine hydroxylase or phenylethanolamine N‐methyltransferase) occurred on many esophageal motor neurons in DMV that had been retrogradely labelled with cholera toxin B subunit (CTB) from the oesophagus. In contrast, all three types of axons very rarely apposed CTB‐labelled motor neurons in NAc. In rats with lentiviral‐induced selective GFP expression in C1, C3 or midline 5‐HT neurons, GFP‐immunoreactive axons were found in close apposition to choline acetyltransferase (ChAT)‐positive DMV neurons, but not ChAT‐positive NAc neurons. This marked difference in innervation indicates that monoamine axons of brainstem origin are likely to be important for controlling the activity of esophageal motor neurons in DMV but not those in NAc. This conclusion is consistent with control of oesophageal smooth muscle by DMV neurons and of oesophageal striated muscle by NAc neurons. Grant Funding Source : NHMRC of Australia