<p><em>Jatropha curcas </em>L. and <em>Jatropha macrocarpa </em>Griseb. (Euphorbiaceae) are perennial species adapted to marginal conditions not suitable for agriculture, and have been recently exploited for oil and biodiesel production<strong>. </strong>The anatomy of different organs in members of this family exhibits a wide range of variations. However, knowledge of anatomical features is still incomplete. The aim of the present work was to analyze the anatomical structure of stem, leaf and root of <em>J. curcas </em>and <em>J. macrocarpa </em>seedling cultivated in a greenhouse. Fixed samples were properly treated using triple stain hematoxylin, safranin and fast green. Primary roots were diarch and triarch in <em>J. curcas</em>, whereas in <em>J. macrocarpa </em>were diarch and the cortex showed parenchyma cells, larger in <em>J. macrocarpa</em> than <em>J. curcas</em>. Stem cortex was thicker in <em>J. macrocarpa</em> than in <em>J. curcas</em>.<em> </em>Both species had parenchyma cells with cystolith, chloroplasts, laticifers and starch granules, these being more abundant in <em>J. macrocarpa</em>. Leaves were characterized by dorsoventral anatomy, with the epiderm showing amphistomatic condition with high stomata density at the lower surface. Both <em>Jatropha </em>species had paracytic stomata. Druses and non-articulated branched laticifers were recorded in the mesophyll. Some of the different anatomical features of <em>J. curcas </em>and <em>J. macrocarpa</em> could explain the different tolerance to abiotic stress.</p>