Abstract: With more and more sequence data available, it has been a widespread practice to apply multiple genes to reconstruct phylogenies at different hierarchical levels. The phenomenon of conflicting gene trees has accordingly become a remarkable and difficult problem. It is increasingly understood that the difference between gene tree and species tree and the causes behind should be fully appreciated in molecular phylogenetic studies. In this paper, we have explored the major causes resulting in conflicting gene trees, including stochastic errors, systematic errors and biological factors. We also introduced a newly developed discipline, phylogenomics, and demonstrated its power and great potential in resolving difficult phylogenetic problems using our recent phyloge-nomic study of Oryza as an example. Furthermore, we discussed some strategies and approaches in elucidating conflicting gene trees and provided some suggestions and recommendations for molecular phylogenetic studies using multiple genes.