Recombination breaks up the evolutionary history between genomic regions and, as a result, the evolutionary history of different genomic regions may differ. In fact, conflicting phylogenetic signal between genes is commonplace. The reasons for conflicting signal may be statistical or systematic in nature. In order to avoid strongly supported but incorrect inferences driven by systematic error, use of appropriate phylogenetic methods accounting for these processes is of fundamental importance. This chapter reviews possible causes of phylogenetic conflict between genes. Processes generating conflict, including gene duplication and loss, horizontal gene transfer, hybridization, and incomplete lineage sorting are presented using classic examples. In particular, we discuss compelling evidence for whole genome duplications in fish, as well as plants, and the role of horizontal transfer in the spread of antibiotic resistance. Finally, building on the material presented, we show how these processes lead to phylogenetic conflict, and how they can be described by phylo-genetic models.