The location and number of neurons in the brainstem with projections to the eye muscles were investigated by means of fluorescent tracers in the African lungfish Protopterus dolloi. The oculomotor nucleus (M III) projects bilaterally with a ratio of 3:1 (70 ipsilateral, 20 contralateral neurons). Three subdivisions of this nucleus can be differentiated: one projects exclusively ipsilaterally, another projects exclusively contralaterally, and a third component projects bilaterally. The trochlear nucleus (M IV) is located caudally, distinct from M III, and projects predominantly to contralateral eye muscles with a ratio of 6:1 (18:3 neurons). The abducens nucleus (M VI) contains about 30 neurons with ipsilateral projections only. There is no evidence for an accessory abducens nucleus in Protopterus. Intraocular injections of tracers do not reveal any retinopetal projections in Protopterus. The mesencephalic trigeminal nucleus (Mes V) of Protopterus and Neoceratodus contains about 540–590 neurons on each side. In juvenile Protopterus, up to 75 Mes V neurons are located caudally in a ventral projection of the tectum above the velum medullare anterius. Fifty-five Mes V neurons (10% of the total number) have processes that exit the brain with the trochlear nerve. The relatively large number of Mes V neurons in lungfishes correlates with the well developed jaw musculature. The present study provides the first conclusive evidence for the location of oculomotor subdivisions in the brain of a lepidosirenid lungfish. The organization of the oculomotor nucleus is consistent with the observation that lungfishes possess the pattern of eye-muscle innervation seen in elasmobranchs and supports the unconventional view that lungfishes may be the sistergroup of elasmobranchs.