Key message ABCE model genes along with genes related to GA biosynthesis and auxin signalling may play significant roles in male flower development inJatropha curcas. Flowering plants exhibit extreme reproductive diversity.Jatropha curcas, a woody plant that is promising for biofuel production, is monoecious. Here, two gynoeciousJatrophamutants (bearing only female flowers) were used to identify key genes involved in male flower development. Using comparative transcriptome analysis, we identified 17 differentially expressed genes (DEGs) involved in floral organ development between monoecious plants and the two gynoecious mutants. Among these DEGs, five floral organ identity genes,Jatropha AGAMOUS,PISTILLATA,SEPALLATA 2-1(JcSEP2-1),JcSEP2-2, andJcSEP3, were downregulated inchmutant inflorescences; two gibberellin (GA) biosynthesis genes,Jatropha GA REQUIRING 1andGIBBERELLIN 3-OXIDASE 1, were downregulated in both thechandgmutants; and two genes involved in the auxin signalling pathway,Jatropha NGATHA1andSTYLISH1, were downregulated in thechmutant. Furthermore, four hub genes involved in male flower development, namelyJatropha SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 1,CRYPTOCHROME 2,SUPPRESSOR OF OVEREXPRESSION OF CO 1andJAGGED, were identified using weighted gene correlation network analysis. These results suggest that floral organ identity genes and genes involved in GA biosynthesis and auxin signalling may participate in male flower development inJatropha. This study will contribute to understanding sex differentiation in woody perennial plants.