Even though the repetitive and decentralized nature of plant organogenesis confers a large plasticity to plants, their architecture is highly organized throughout ontogeny and at different scales. Growth, branching and flowering constitute the main processes leading to plant architectures and are key determinants of plant productivity, whatever the target product (biomass, flowers, seeds or fruits). Their genetic and genomic study is thus of great interest for breeding purpose. However, progresses have been limited by many constraints resulting from the large size and long-live of trees and therefore the difficult to assess phenotypes on large numbers of individuals for exploring both the genetic effect or genetic by environment interaction. Despite these limitations, significant advances have been recently obtained in quantitative genetics studies performed on architectural traits in forest and fruit trees, and on the physiological and molecular comprehension of mechanisms underlying plant architectural edification. Moreover, tools and methods for describing plant architectures and for exploring genetic and molecular controls have been improved, leading to new perspectives in terms of high-throughput genotyping, phenotyping and genomic studies. In this chapter, we review the genetic, physiological and molecular analyses that have been performed in the last years on tree architecture, with a particular focus on advances realized on tree crops.