This chapter explores the causes of discordance between gene trees and species trees. Processes such as hybridisation, selection, incomplete lineage sorting, sharing of ancestral polymorphism and short internodes are described as sources of conflict. Gene divergence predating species divergence is also explained as one of the reasons that might complicate phylogenetic inference. With respect to incomplete lineage sorting, the link between effective population size of the markers and monophyly is explored. Examples illustrate how single-locus analyses can misrepresent species histories. The chapter emphasises multi-locus and coalescent-based approaches as solutions, urging caution when interpreting individual gene trees. It provides a conceptual framework for understanding why phylogenetic trees can differ across markers and how to reconcile them to recover accurate species histories.