For centuries olive tree is an important crop in many Mediterranean countries because it provides appreciated oil with healthy properties. The lack of genomic tools, such as molecular markers or sequence information, has hindered the development of new cultivars adapted to the challenges that this species faces due to the change in modern cultivation practices, such as the increase in the number of trees per hectare. This tree has an excessive vigour that can be a serious economic limitation for intensive or super-intensive orchards. These and other issues have been recently addressed by a number of scientific efforts. This review will give a broad view over the recent genomic developments in olive tree, and the plant architecture as a complex trait.