To verify the possible morphological and ultrastructural differences in the Jatropha curcas leaves, in response to high-intensity salt stress, three genotypes were evaluated (CNPAE183, JCAL171, and CNPAE218). In all the genotypes, 750mM NaCl, added to the nutrient solution, was applied to test its salt tolerance. For the analysis, the leaves were collected at three time points: (i) before stress (time 0 hour); (ii) during stress time (time 50 hours); and (iii) in the recovery period (time 914 hours) when the stressed plants recovered and demonstrated measurements of net photosynthetic with values similar to those demonstrated by the control plants. We showed that regardless of the genotype, saline shock caused an increase in the thickness of the mesophyll, and after the removal of NaCl, the thicker mesophyll remained in the JCAL171 and CNPAE218 genotypes, while the values observed in the CNPAE183 genotype were similar to those before stress. Scanning electron microscopy indicated that the stomata of CNPAE183 are smaller and have a stomatal index higher than the values demonstrated in JCAL171 and CNPAE218. Therefore, among the genotypes analyzed, CNPAE183 demonstrates that it could be considered a promising genotype for future studies of genetic improvement that seek elite genotypes tolerant to salinity.