Geometric morphometric analysis was used to describe the variations in body shape existing in Sardinellafimbriata sampled from Butuan Bay, Dipolog Bay, and Pagadian Bay in Mindanao, Philippines. A notable degree of significance was detected both within and between populations which is shown by the results obtained from multivariate analysis of variance (MANOVA), canonical variate analysis (CVA), and discriminant function analysis (DFA). Within populations showed sexual dimorphism between the two sexes while geographic isolation may have caused the variations that were detected between the three populations. Additionally, environmental factors such as overfishing/overexploitation and different methods of fishing could also be one of the factors causing these variations. Hence, this study proved the ability of modern geometric morphometrics to distinguish and describe body shape variations existing within and between populations of S. fimbriata. It is recommended, however, that a genetic study regarding these shape variations should be as well conducted to understand more the diversity of this species which would greatly contribute to mananagement strategies of stocks or populations of S. fimbriata.