The black rockfish (Sebastes schlegelii) is an important economic fish species widely distributed across the coastal areas of northern China. It has been widely studied due to its special viviparous reproductive strategy and long-term sperm storage characteristics. Although there are some previous reports about multiple paternity in S. schlegelii, the spatial distribution pattern of paternity in the ovary has not been studied. In this study, the multiple paternity in different regions of the ovary was investigated by applying six polymorphic microsatellite markers to genotype 9 cultured pregnant females and 291 of their offspring in different regions (the proximal part from the cloacal orifice, the middle part, and the distal part) of the ovary in S. schlegelii. The results showed that: (1) Multiple paternity was detected in 8 of 9 (88.89%) cultured female fish, which was similar to the findings of reports of the previous two scholars whose work focused on cultured and wild black rockfish. However, the average number of copulations was 3.56 times, which was higher than that reported in previous studies. The reason for this phenomenon might be the higher group density (7–8 fish/m3 ) than in previous studies. Furthermore, four broods were significantly skewed from equal paternal contributions (50%, B>0); (2) the results of one-way ANOVA showed that the proportions of paternal offspring did not significantly differ in the different regions of the ovary in females; and (3) the chi-square uniform distribution test results showed that the paternal offspring in each family had no significant bias in different ovary regions, indicating that multiple paternity in S. schlegelii is randomly distributed in the ovary due to a degree of sperm mixing in the female’s ovaries after mating to some extent. Considering that the ovaries of female fish are not yet mature in S. schlegelii during the mating period, the sperm from different males may be completely mixed in the immature ovary and then stored in it. The differences in males’ sperm number and sperm activity may be the important reasons for the bias of paternity contribution rate. These results may provide a scientific basis for the enrichment of reproductive biology research on S. schlegelii.