The yellow drum (Nibea albiflora) is an important marine fish and has been cultured widely in Southeast China in recent years. To understand the gene homozygosity of meiotic gynogens of yellow drum, microsatellite markers (SSR) and amplified fragments length polymorphism (AFLP) markers were applied to identify gynogenetic diploid offspring and genetic analyze. The results showed:(1) no paternal specific alleles were found in all 4 SSR loci or amplification loci from five pairs of AFLP selective primers in the gynogenetic diploid family, indicating that all individuals in the gynogenetic diploid family were gynogens; (2) no completely homozygous loci were found in seven SSR loci in either gynogenetic diploid family or normal mating family. The average homozygosity of the gynogenetic diploid family was 0.382, 2.37 times that of the normal mating family (0.161). Homozygous loci in gynogenesis individuals was during 0-6, with their homozygous ratio of 0-85.7%, whereas the homozygous loci in normal individuals was during 0-4, with their homozygous ratio of 0-57.1%; (3) 182 clear bands were amplified from five pairs of AFLP selective primers, of which there were 21 paternal and 16 maternal specific bands. Among the 16 maternal specific bands, ten bands were heterozygous loci, and seven loci in the gynogenetic diploid family showed significant partial separation (P<0.05). The percentage of polymorphic bands in the gynogenetic and normal mating families were 14.7% and 20.3%, respectively; (4) based on SSR and AFLP markers, the gynogenetic diploid family had a higher genetic similarity to female parents than to the normal mating family, whereas the normal mating family had approximately the same genetic distance to both parents. The results showed that the genetic homozygosity of the meiotic gynogenetic diploid family was significantly higher than that of the normal mating family, and artificial induction of gynogenetic development is an effective way to promote gene homozygosity, since it can accelerate favorable homozygous gene fixation, and also accelerate harmful gene elimination; thus, effectively improve breeding efficiency.