Many environmental factors affect the morphology of migratory fish species, such as salinity, water flow rate, and temperature. However, studies on changes in fish morphology under environmental variations from salt water to brackish water are still limited in many fish species, especially in *Terapon jarbua*. This study aims to investigate the differences in the morphological parameters of *T. jarbua* between the coastal sea (seawater) and lagoon (brackish water); and between male and female fish based on a landmark morphological approach. Additionally, the genetic diversity of *T. jarbua* populations in Central Vietnam was elucidated using the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) sequence as a molecular marker. The analytical results indicated no sexual dimorphism in the *T. jarbua* population, yet conformational differences exist between the two studied aquatic species. The analysis of 42 mtDNA COI sequences collected from Central Vietnam identified 13 haplotypes with medium genetic diversity and low genetic differentiation between the Tam Giang lagoon and Thua Thien Hue coastal (Fst = 0.028) and not significant (p = 0.126). Most haplotypes obtained are present in reference populations, indicating a high genetic exchange between populations. We proposed that the *T. jarbua* population in Central Vietnam has a stable connection with neighboring populations (China, Taiwan, Philippines, Indonesia, Malaysia, Bangladesh, India, and Pakistan)
