Providing parental care for offspring has been shown to benefit parents if it increases offspring survival, growth and quality of offspring, however, caring for offspring is energetically expensive, and effort spent on raising unrelated offspring can be costly and wasteful. Theory dictates parents should reduce their level of investment when they have low or uncertain relatedness to the young under their care in favour of alternative broods that provide greater reproductive success. We tested these ideas using Plainfin midshipman fish, Porichthys notatus, a species that exhibits polymorphism with two male morphs, a high level of cuckoldry, and an extended period of male-only parental care. We investigate parental care cost theory to test whether paternal investment is reduced as perceived paternity decreases given indirect cues for paternity assessment. We show that males with eggs demonstrate a greater level of parental care, including defensive behaviours, than males without eggs. However, no significant difference was determined between levels of parental care provided by males with reduced levels of paternity. Despite the theoretically established relationship between parental certainty and parental care, experimental manipulations of perceived paternity continue to generate mixed results. The apparent lack of effect of paternal certainty on paternal care presents a challenge to the current understanding of the relationship between the costs and benefits of parental care in males with uncertain paternity.