Abstract: The aim was to provide a theoretical basis for pigmentation mechanism of leaves and flower of Anthurium andraeanum. Anthurium andraeanum ‘Alabama’ was used as the material, the AaPDS gene was cloned by RACE, and expression analysis was performed by RT-PCR. AaPDS cDNA sequence consisted of 2226 bp with an intact open reading frame of 1767 bp, encoding 588 amino acids. Analysis of sequence alignment indicated that AaPDS sequence had 74%-79% identity with those of Narcissus tazetta, Strelitzia reginae, Nicotiana tabacum, Vitis vinifera, Hydrilla verticillata, Helianthus annuus et al. Phylogenetic analysis indicated that AaPDS was clustered together with those of moncotylous plants, such as Hydrilla verticillata, Oryza sativa, Narcissus tazetta and Strelitzia reginae et al. RT-PCR analysis indicated that AaPDS showed the greatest expression in the spadix, then the expression was gradually reduced in spathe, leaf, stem and root. Taxonomy results obtained by molecular biology were consistent with those by traditional methods. The PDS gene in carotenoids metabolic pathway played some a certain role in the organ pigmentation of Anthurium andraeanum.