Acacia mangium Willd. is a legume tree species native to subtropical and tropical regions of Asia and Australia. Many features of its flower development are common to other legume tree species. To identify genes involved in its floral development, we constructed a subtractive flower cDNA library against vegetative tissues. The 1123 expressed sequence tags (ESTs) represented 576 unique genes. Macroarray analysis further identified 147 of these genes as specific to the early, late or whole flowering process. Eight percent of these flower-specific genes encode MADS-domain-containing transcription factors and MYB proteins. Four percent encode other transcription factors and 10% encode regulatory proteins such as G proteins, kinases and phosphatases. Flower-specific transcripts for gibberellic acid (GA) synthesis and GA-induced proteins, as well as other stress- and pathogenesis-related genes (9%), implicate their involvement in A. mangium flower development. Eighteen percent of the flower-specific genes encode hypothetical proteins and 18% encode proteins of unknown functions. The RNA blot hybridization confirmed and detailed the expression patterns of selected genes. Functions of the A. mangium flower-specific genes are discussed based on comparison with their Arabidopsis homologues, most of which have been implicated in Arabidopsis floral development. Our work suggests general conservation of floral development in A. mangium and Arabidopsis. Further characterization of the conserved and different flower-specific genes will delineate the flowering process of this important legume tree species and facilitate genetic modification of its reproduction.