In fish with paternal care, protogynous sex change (female to male) is rare and has only been reported from species with haremic polygyny. The swamp eel, Monopterus albus, is a protogynous fish with paternal care, but little is known about its mating system. To understand protogyny in this species, we examined the mating system and male size advantage in mating in M. albus under semi-natural condition. Females swam over wide ranges and visited multiple male nests. Males defended a narrow territory around nests against other males that approached nests; at these nests, males courted and accepted visiting females. After spawning inside nests, caring males continued to perform courtship activities, and multiple breeding was observed. These observations suggest that the M. albus mating system is male-territory-visiting (MTV)-polygamy. Larger males had nests, and mated more frequently compared with small males. Because small initial males of this species are not found in nature, and because M. albus does not engage in sneaking tactics, larger nesting males do not suffer from reproductive parasitism. Thus, protogyny in this fish is likely consistent with the predictions of the size-advantage model. Biting attacks by territorial males of this predatory fish seriously wounded intruding males, occasionally resulting in the death of the intruder. We discuss the possibility that sexual differences in mortality rates in small fish may facilitate the evolution of protogyny in this species. Protogyny of the swamp eel is, to our knowledge, the first example of an MTV-polygamous mating system in a fish with paternal care.