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Jatropha has gained interest as a potential biodiesel feedstock. Nevertheless, its oil production decreases significantly in frost- and drought-prone regions. In this study, we characterized the flowering pattern of Jatropha in Botswana in the 2014/2015 season. Extensive springtime pruning synchronized Jatropha regrowth in summer and effectively stimulated growth after frost damage. Flowering started in February 2015 and peaked in April and May. Wide variations in flowering frequency were observed among different Jatropha accessions. Trees flowering in February and March produced fruit in May, but most trees only flowered in April and May and did not yield fruit because of cold snaps. These observations suggested that harvesting seed before wintertime is the key to improve Jatropha production in the Botswana climate. This study highlighted the importance of inducing early flowering by developing new agricultural managements. These may include frost cover and sun shades to prevent stress-induced damage, canopy control by pruning, optimization of fertilization practice, and/or introduction of superior Jatropha varieties.