A comparison of external morphology captured via a computer vision system and a study of internal anatomy of sweetpotato somatic embryos identified five different major morphological variants among torpedo and cotyledonary stage embryos. These included 1) Perfect Type, 2) Near Perfect Type, 3) Limited/No Meristematic Activity Type, 4) Disrupted Internal Anatomy Type, 5) Proliferating Type. Perfect and Near Perfect types of somatic embryos were categorized as competent, while Limited/No Meristematic activity, Disrupted Internal Anatomy, and Proliferating types were categorized as noncompetent with respect to their conversion ability. Lack of organized shoot development in somatic embryos of sweetpotato was attributed to the following abnormalities: 1) lack of an organized apical meristem, 2) sparsity of dividing cells in the apical region, 3) flattened apical meristem, 4) multiple meristemoids and/or diffuse meristematic activity throughout the embryo. A morphological fate map of most of the torpedo and cotyledonary embryo variants was identified, which will be beneficial in synthetic seeding and transgenic research and development of sweetpotato.