To estimate the heritabilities of growth-related traits in large yellow croaker, Larimichthys crocea, three independent full-factorial crosses were created by crossing four males × four females, seven males × three females and four males × three females (set 1, set 2 and set 3). At 13 months post-hatch, the juveniles were collected from three cross sets and measured for body mass (M), standard length (LS) and body height (HB). In addition, the parentage of the juveniles was assigned by genotyping six or seven polymorphic microsatellite loci. Out of the 959 juveniles, 99·6% could be assigned to a single parental pair. Heritabilities of growth-related traits were estimated for individual and combined sets with the pedigrees reconstructed by using microsatellite genotypes. The heritability estimates at 13 month-old were 0·02–0·30 for M, 0·02–0·25 for LS and 0·03–0·36 for HB. These results showed that the heritabilities of M, LS and HB were different among three sets, which suggested that different breeding strategies should be adopted for different sets.