Group spawning (1 female and more than 2 males) and streaking behaviour of subordinate males are common in pelagic-spawning reef fishes such as the temperate tetrarogidid fish Hypodytes rubripinnis. Five microsatellite loci were isolated and characterized for paternity analysis of this species. Four of the five loci were highly polymorphic, having 11–34 alleles with observed heterozygosities between 0.89 and 1.00 in 37 unrelated individuals. These four loci conformed to Hardy–Weinberg equilibrium. These loci should be useful in future studies that assess how fertilization is partitioned among male H. rubripinnis in multimale spawning events.