Like many other gobies, males of the Isaza goby, Gymnogobius isaza endemic to Lake Biwa, Japan, conduct parental care of eggs at nests, and females are likely to choose mates while visiting nests. The reproductive strategy should induce polygyny, but Isaza males never accept additional females in one breeding cycle. Sampling data of broods indicated that the egg mass areas were much smaller than the nest sizes, suggesting that nest size is not the limiting factor in obtaining further eggs from additional females. The brood size greatly decreased as the duration of care progressed. Few individuals including caring males ate eggs, and heterospecific egg predators were rarely observed. Sixty percent of egg masses at the middle stages of egg development were infected with aquatic fungi, some being covered with a fungus mat that drastically reduced survivorship. Infected egg masses contained more eggs than non-infected ones at the same stage, indicating that large egg masses are prone to be frequently destroyed by fungi. It is likely that the activity of parental males is lowered during the long care periods at low water temperature in early spring. Such lowered activity of caring males might be responsible for infections in large broods that would have needed more care. We propose the hypothesis that male rejection of additional females may be related to optimal brood size, which will be less susceptible to fungus infection and produce more hatching young than otherwise. This hypothesis will explain not only male avoidance of additional females but also some unique reproductive behaviors of this fish such as some females' spawning of a portion of of the mature eggs in one nest.