In production, most cultivars of melon are andromonoecious and characterized by carrying both male and bisexual flowers on the same plant. In this study, four A-class genes (CmAP1a, CmAP1b, CmAP2a and CmAP2b), two B-class genes (CmAP3 and CmPI), two C-class genes (CmAGa and CmAGb) and four E-class genes (CmSEP1,2,3,4) were identified in melon. However, no D-class gene of melon was identified. The conserved domains of ABCE function proteins showed relatively high similarity between Arabidopsis and melon. The expression patterns of ABCE homeotic genes in different flower buds of melon suggested that transcripts of CmAP1a, CmPI and CmSEP1 in bisexual buds were significantly lower than that in male flower buds, while the expression levels of CmAGa, CmAGb and CmSEP4 in bisexual flower buds were significantly higher than that in male flower buds. There was no significant difference in expression levels of other ABCE model genes between male buds and bisexual buds. Subsequently, qRT-PCR was performed in different floral organs of bisexual flowers in melon. For A class genes, CmAP1a and CmAP1b showed the highest accumulation in sepals than petals, stamens and pistil, while CmAP2a and CmAP2b revealed the highest expression in pistil than other three floral organs. For B class genes, CmAP3 and CmPI were highly accumulated in petals and stamens though CmAP3 also showed abundant accumulation in pistil. For C class genes, the expression levels of CmAGa and CmAGb were higher in stamens and pistil than that in sepals and petals. For E class genes, CmSEP1 showed higher expression level in sepals and petals than stamens and pistil. CmSEP2, CmSEP3 and CmSEP4 showed the highest accumulation in pistil than other floral organs. These results provided a theoretical basis for studying the function of ABCE homeotic genes in floral organs development of melon.