There has been much interest in the development of embryogenic systems in woody plants, aimed at optimizing efficient genetic transformation methods to incorporate useful genes. Among the different regeneration systems, embryogenic cultures have been the most responsive tissues with competence for in vitro regeneration and genetic transformation. We present an overview of woody plant biotechnology and cover culture systems, methods of transformation, selectable marker genes and some selected case studies representing forest and fruit crops: sandalwood, conifers, acacia, grape, mango, avocado, rubber and walnut. The development of transgenic systems in these plant species is expected to contribute to their overall improvement in wood quality, resistance to diseases and pests and tolerance to environmental stress.