In species in which paternal care of offspring is important but paternity is uncertain, evolutionary theory suggests that kin recognition mechanisms (e.g. phenotype matching) should evolve. Fathers are expected to discriminate between their children and others’ on the basis of phenotypic similarities, and they should allocate resources accordingly. However, studies showing that males assess paternity by phenotype matching are rare. In a polygynous human population of rural Senegal, we examined the relationships between (1) actual father–child resemblance through both the facial and the olfactory phenotypes; (2) fathers’ investment of resources in each child; and (3) child nutritional condition. We found that paternal investment was positively related to both face and odour similarities between fathers and children. Additionally, such discriminative paternal investment was linked to the children’s health: children who received more investment had better growth and nutritional status. This is the first evidence that paternal investment is associated with father–child resemblance in real human families, and, furthermore, that these discrepancies in paternal investment result in differences in fitness-related traits in children.