Abstract: In both plants and animals, distant hybridization often gives rise to offspring exhibiting hybrid vigor, and this approach has shown significant potential in aquaculture. Grouper, an economically important marine species, has experienced rapid industry development. To cultivate new grouper varieties of high economic value, a crossbreeding experiment involving Epinephelus fuscoguttatus (♀) and Epinephelus polyphekadion (♂) was carried out, resulting in the successful production of hybrid offspring. External morphological analysis is the most straightforward indicator, influenced by genetics and the environment, playing a pivotal role in subsequent fish breeding. Investigating population morphological differences holds practical significance for understanding population structure composition and environmental effects, as well as providing guidance for fisheries resource management. Due to the similar physical appearance of E. fuscoguttatus and E. polyphekadion, distinguishing the hybrid grouper from its parents species proves to be challenging. In order to explore both phenotypic and genetic differences between parents and the hybrid, we utilized the external morphological and frame parameters for comparative analysis. In the exploration of external morphological structures, the results of cluster analysis and principal component analysis both indicate that the quantitative traits and external framework of the hybrid offspring tend to resemble those of the maternal E. fuscoguttatus. During hybridization processes, especially in cases of distant hybridization, each parent contributes one gamete, and these gametes undergo meiosis during formation. Allelic genes on homologous chromosomes segregate from each other, while non-allelic genes on non-homologous chromosomes freely recombine. Consequently, genetic loci controlling dominant traits often display incomplete dominance during the hybridization process, giving rise to new genotypes that combine and express dominant traits in the hybrid offspring. Distant hybridization frequently results in offspring with increased genetic diversity, which can establish the foundation for breeding and genetic improvement in both animals and plants when evaluated. Therefore, we used simple sequence repeat (SSR) analysis to assess the genetic characteristics of both parental and hybrid offspring. A total of 6266 SSRs were identified via ddRAD-seq for E. fuscoguttatus, among them, seven pairs of SSRs were screened, which could be stably amplified in parental and hybrid population and had high genetic diversity. The observed heterozygosity (Ho), the expected heterozygosity (He) and the polymorphic information content (PIC) of the seven SSRs in the hybrid population were 0.891, 0.768 and 0.717, respectively. These values were notably higher than those observed within their respective parental populations, indicating that the hybrid offspring exhibit an enhanced genetic diversity in terms of genetic information. The research findings can provide methods for distinguishing between E. fuscoguttatus and E. polyphekadion and their hybrid offspring, as well as offering a theoretical foundation for the cultivation of hybrid groupers.