<p>Acerola (Barbados cherries) has become a highly traded superfruit because it contains many phytonutrients and is a good source of vitamin C. The fruits of <i>Malpighia glabra</i>, and <i>M. emarginata</i> are utilized in food products, dietary supplements and natural health products. However, there are differences among the fruit of <i>Malpighia</i> species with respect to phytochemicals, nutrient value and clinical research. Furthermore, there is evidence of adulteration with other fruit such as cherries (<i>Prunus</i> spp.). Unfortunately, conventional morphological examination does not distinguish acerola fruit species. Furthermore, no published methods are available to distinguish the fruits of these species including chemical and DNA based techniques. This risk to quality assurance (QA) is increased when considering processed berries into juice or powdered ingredients of which are the most common source for manufactures. This lack of QA methods also increases the risk of adulteration with cheaper fruit from other species. The goal of this research is to provide orthogonal molecular methods to authenticate Acerola fruit ingredients and discuss the benefits and constraints of these two different methods. This research supports quality assurance (QA) programs with fit-for-purpose methods for verifying the authenticity of acerola species ingredients from suppliers.</p>