Instability of papaya flowers is revealed by environmentally influenced sex reversal and stamen carpellody that is responsible for malformation of fruit, making them unmarketable. Based on knowledge of flower development in the model plants Antirrhirum and Arabidopsis, papaya homologous genes associated with flower development were cloned and characterized. The homologous genes FLOR/CAULA (FLO) in Antirrhirum and LEAFY (LFY) in Arabidopsis are known to regulate the initiation of flowering and the expression of floral organ identity genes. The papaya LFY homolog, PFL, shares 61% and 67% identity with LFYand FLO, respectively. Despite extensive sequence similarity in two conserved regions, the proline-rich motif differs between PFL and its counterparts in other plant species. This difference may not affect the gene function as demonstrated by the Pinus radiata LFY homolog, Need/y. Genomic and BAC southern analyses indicated only one copy of the PFL in the papaya genome. /n situ hybridization result revealed that PFL was already detected in the shoot apical meristem (SAM) of young seedling at 5-node stage and it was expressed at a relatively lower level in leaf primodia, and at a high level in floral meristem. The C class gene AGAMOUS (AG) is required for both stamen and carpel identity. The AG homolog in papaya, PAG, was cloned and its full-length cDNA sequence and partial genomic sequence were obtained. PAG has 9 exons with a large, 6-7kb second intron and shares about 98% and 71% identity with the Arabidopsis AG MADS box and K box regions, respectively. Southern hybridization result shows only one copy of the PAG gene in the papaya genome. Northern analysis indicates PAG is expressed in flowers from a very early stage of flower development through mature flowers, but not in roots and leaves. HUA1 homolog in papaya, PHUA1, another regulator of stamen and carpel identities, shares 62% identity and 74% similarity with Arabidopsis HUA1. In the deduced amino acid sequenc.