Abstract: Hermaphroditism occurs in many fish species, yet self-fertilization remains rare. As an extreme form of inbreeding, selfing offers a rapid method to establish pure lines for breeding purposes. Black porgy (Acanthopagrus schlegelii), a commercially important marine fish widely distributed along the coast of China, is a protandrous hermaphrodite. Individuals are functionally male at 1—2 years of age, with about 30% undergoing sex reversal to females at age 3. By cryopreserving sperm from a male-phase individual and later using it to fertilize eggs from the same individual after it becomes female, self-fertilization can be achieved. This approach offers a novel strategy to accelerate genetic improvement in the species, with important implications for developing new breeding models and overcoming the persistent shortage of improved varieties in aquaculture. To examine genetic changes in self-fertilized offspring of black porgy, whole-genome resequencing was used to analyze single-nucleotide polymorphisms (SNPs) and homozygosity in three selfed families (BP246, BP291, and BP384). Across the three families, 3991267 SNP sites were identified, the largest proportion (47.42%) of which were located in introns. The average proportion of homozygous sites in offspring was 69.11%, significantly higher than in parents (38.49%). Observed heterozygosity (H_o) values for BP246, BP291, and BP384 were 0.2986, 0.2875, and 0.2805, respectively-all lower than the corresponding expected heterozygosity (H_e) values (0.3947, 0.3946, and 0.3946). Analysis of F_st, principal components, and phylogenetic trees revealed high genetic differentiation among the offspring families. A total of 10991 runs of homozygosity (ROH) were detected in offspring, with short fragments (<1 Mb) accounting for 52.5% and long fragments (>2.5 Mb) for 9.4%. Thirteen ROH islands (high-frequency homozygous regions) were identified on five chromosomes, encompassing 468 annotated genes. 64 candidate genes were significantly enriched and potentially linked to traits such as growth and immunity. These genes were primarily involved in calcium signaling (e.g., CACNA1S), energy metabolism (AMPD, ADCY5/6), DNA repair (RAD18), and immune regulation (PIK3CA_B_D). The findings provide a scientific basis for refining black porgy breeding strategies and advancing genetic research on self-fertilization in fish.