This study was conducted to investigate the intraspecific variation of Eleutheronema tetradactylum (Shaw, 1804) using traditional morphometric measurements. In total, 136 samples were collected from four fishing areas across Thailand coastal waters. Raw data were standardized and then evaluated with univariate analysis of variance, canonical discriminant function analysis, and dendrogram of cluster analysis regarding to site, size, and sex. Result from ANOVA test exhibited that all morphological characters were significantly different among sites (P < 0.05). Nevertheless, forty-one morphometric characters were significantly different among size of male and female fish (P < 0.05) except for pre-orbital length, pupil diameter, eye diameter, and depth of maxilla for male fish. Forty-four morphometric characters were significantly different (P < 0.05) except of fork length among sex. From CDFA, E. tetradactylum showed phenotypic heterogeneity and two distinct stocks in the four selected fishing areas. Phenotypic variation on sites was determined by six morphological characters (MnFL, DFAF, DOM, HW, PeBFL and ED) for males, while eight characters for females (PrOL, AFSL, PeBFL, DOM, UJL, PD, AFRL and ED) in decreasing order. Differentiations between fish size classes, relied on PrDFL2, BD and UCFL in males and PrOL, PrePeFL and DFAF in females. Among sexes, PeFAF, PrDFL2, MxFL, MnFL, PrePeFL, HSDF and PrePFL were highly influential. Discriminate functions (DF1) clarified that 83.60% and 94.10% of the total variance were found among the sites of males and females, and 99.20% and 93.20% of the total variance were found among the sizes of males and females, respectively. and 73% of the total variance were found among the sexes. In the confusion matrix of CDFA, the overall assignments of individuals into their correctly classified original population were 98.68% and 100% for males and females based on site and size, and 75.74% of sex groups, respectively. Our study highlighted that the hermaphroditism of E. tetradactylum showed that three distinct stocks of males and two stocks of females inhabited Thai coastal waters.