Geometric morphometry is applied to discriminate the three species of stingless bees (Trigona (Tetragonula) iridipennis, Trigona (Tetragonula) aff. laeviceps and Trigona (Lepidotrigona) ventralis var. arcifera). The present study characterized the three species by using the relative wrap analysis, the three species forms three distinct groups and the Principal Component Analysis (PCA) explained that there are 90.29% of the variations and forms three distinct clusters within these three groups. The multivariate analyses of variance (MANOVA) are showed that the stingless bee forewings indicate significant differences (P < 0.0001).