Abstract: Hippocampus abdominalis was the largest known species of seahorse, primarily distributed in the sea of Australian and New Zealand. It has been included in the Red List of the World's Threatened Species due to overfishing, deterioration of the marine environment and global warming. It has been bred in captivity and was introduced to China in 2016. Current research primarily focused on reproductive physiology, pharmacological effects and aquaculture ecology. In the actual production and breeding of H. abdominalis, there are generally significant differences in growth traits in the same batch of seahorse populations. The breeding enterprises need to be screened regularly according to the size of the specifications to facilitate breeding management. The screening process is not only easy to cause the stress reaction of H. abdominalis but also increase the burden of production and breeding. Growth traits are important economic traits in aquatic animal genetic breeding. Therefore, combining trait molecular markers with breeding methods can improve breeding efficiency, accelerate breeding process and improve uniformity. To screen molecular markers related to growth traits of H. abdominalis, this study combined BSA and SSR techniques to screen differential growth trait markers of the same age H. abdominalis population cultured in the same pond. Firstly, the 4 Mb growth trait candidate region was initially mapped using BSA resequencing. Then, MISA tool was used to search for microsatellite locus in this candidate region and 16691 primers were designed. 273 primer pairs were selected for amplification analysis of two gene pools constructed from 60 individuals with fast and slow growth in H. abdominalis. A total of 55 differential locus were screened, and the genotype differences of these 55-differential locus in these 120 individuals were analyzed. The results showed that there were significant positive correlation (P<0.05) between allele fragments of 266 bp, 245 bp, 303 bp and 338 bp at locus HA81, HA88 and HA223 and growth traits, with correlation coefficients of 0.202, 0.183, 0.219, and 0.235, respectively; There were significant negative correlations (P<0.05) between allele fragments of 263 bp and 260 bp at locus HA88 and HA223 and growth traits, with correlation coefficients of -0.181 and -0.420, respectively; Finally, pedigree individual verification was conducted on these 3 locus, and the results showed that locus HA81 and HA88 were significantly positively correlated with growth traits at the 266 bp and 245 bp allele fragments, respectively, while locus HA223 was significantly negatively correlated with growth traits at the 260 bp allele fragment. Therefore, this study obtained for the first time 3 molecular markers significantly correlated with the growth traits of H. abdominalis, providing a reference for molecular marker assisted breeding of H. abdominalis growth traits.