This paper contributed data on otoliths morphometry and their relationships with the size of Periophthalmodon septemradiatus. A total of 135 specimens (86 males and 49 females) were collected from the five sites in branches of the Bassac River, Vietnam. Length, width, and weight of left otoliths were similar to those of the right otoliths. These otolith parameters of did not change with gender, but vary significantly in five sites, reaching the highest point in the upstream of Bassac River in Binh Duc, Long Xuyen, An Giang where fish total length and body weight reached the highest values. The otolith length, width, and weight had strong relationships with fish total length and body weight due to the high value of determination coefficients (r²). Among the three dimensions of otoliths, otolith length was the most positive relationship with fish size since r² of this regression reaches the highest value. The results suggested that otolith dimensions could be used for fish size determination