Jatropha (Jatropha curcas) is one of the most popular tree crops for seed production as a source of oil for biodiesel. However, currently grown cultivars are too large in canopy size and thus have very low harvest index. Alteration of canopy height and size can lead to identification of a desirable plant architecture for jatropha. A study was conducted to determine genetic control of dwarfiness and erect growth habit in jatropha populations derived from an interspecific cross between J. curcas with tall-erect (TL-ER) plant type and J. integerrima with dwarf-spreading (DW-SP) plant type. Crosses were made between both species to develop F1, F2, BC1F1, and BC1F2 generations. The F2 plants segregated at a 1:2:1 ratio for tall (TL), intermediate (ID), and dwarf (DW) plant types as well as for spreading (SP), upright (UP), and erect (ER) canopy angles. Both characters segregated independently producing nine phenotypes including TL-ER, TL-UP, TL-SP, ID-ER, ID-UP, ID-SP, DW-ER, DW-UP, and DW-SP at a 1:2:1:2:4:2:1:2:1 ratio. The BC1F1 (J. curcas × F1) plant segregated into TL-ER, TL-UP, ID-ER, and ID-UP at a 1:1:1:1 expected ratio. Six BC1F2 lines were also evaluated to confirm the results by selfing two trees each of BC1F1 showing TL-ER, TL-UP, and ID-ER growth habits. The progenies of TL-ER trees were all TL-ER; the progenies of TL-UP trees segregated into TL-ER, TL-UP, and TL-SP at an expected 1:2:1 ratio, whereas the progenies of ID-ER trees segregated into TL-ER, ID-ER, and DW-ER at an expected 1:2:1 ratio. The results indicated that dwarfiness and erect growth habit were each controlled by independent genes with incomplete dominant action. The knowledge and progenies obtained from this study can be used in breeding jatropha for desirable canopy size and shape.