Geometric morphometric techniques were used to assess possible ecotypes within four species of African stingless bees from three different ecological zones in Ghana. Canonical Variate Analyses, Discriminant Analyses, Principal Component Analyses among other techniques evaluated shape variations of eight homologous landmarks on right forewings and effectively discriminated 16 possible ecotypes among 39 populations of stingless bees. It is therefore recommended to stakeholders in meliponiculture to consider the results of this study when exploring movement of colonies from one ecological zone to another.