The life cycle of a seed plant involves subsequent stages of development including germination and seedling establishment. Morphological structures have a fundamental role in these phases, since they are strongly related to physiological adaptations to survival in a range of environments. The present study describes an important morphophysiological and anatomical pattern in embryos of Jatropha genus, involving adaptations for germination and seedling growth. Seed embryos of Jatropha curcas, J. gossypiifolia, J. podagrica and J. multifida were examined using different physiological and microscopic assays. Jatropha species present a multimeristematic embryo composed of one main apical primary meristem plus four radial primary meristems. Seed germination is completed by simultaneous protrusion of five functional roots and seedlings are able to survive even with only one of them. The hypocotyl-radicle transition zone exhibiting different stomata sizes, ontogenic phases and short lifespan limited to the germination. Stomata fractures at mid-region due to the fact that guard cells were not lengthen as neighboring epidermal cells, forming a large cavity in the epidermal tissue during seedling growth. The results showed an unusual and complex root structure for the Jatropha genus. The presence of stomata operating strictly during seed germination could be associated to intense energetic metabolism demanded for the simultaneous growth of the five roots originated from the multimeristematic radicle. This study provides important insights into the understanding of seed germination of Jatropha species in response to stress environmental conditions.