Conservation of genetic diversity of forest tree species in Croatia is based on maintaining sustainable forest management and conserving the structure of natural forest stands, currently making 95 % of the total woodland area.

Croatia is geographically very diverse and therefore its forests formed various ecological types sensitive to habitat degradation, air and water pollution, excessive use of certain more valuable species of forest trees, as well as other anthropogenic effects, increasing impact of global climatic changes. The majority of forests are state owned and managed by Croatian Forests Co., which are financing research conducted by Faculty of Forestry, University of Zagreb and Croatian Forestry Research Institute, within the Research Work Programme on Management and Conservation of forest genetic resources.

The genetic conservation of forest trees was initiated by the EUFORGEN programme started in 1994. The principles of genetic variability are incorporated in management of economically most utilized social broadleaves species (Quercus robur, Quercus petraea, Fagus sylvatica). Among the conifers, silver fir (Abies alba) is the most endangered species, with more than 70 % of its population being permanently damaged. Other native coniferous species must be preserved from a decrease in genetic variability as well. Conservation of the noble broadleaves should encompass a larger number of species from various genera (Fraxinus, Alnus, Ulmus, Prunus, Juglans, Castanea, Sorbus, Acer, Malus, Pyrus, Tilia). These are partially endangered because of their exposure to different diseases and pests, as well as by permanent exploitation due to their technical value.

Changes in hydrological conditions of main rivers have brought about difficulties in regeneration of the riparian forests, and decreased genetic variability of European black and white poplar (Populus nigra, P. alba) in their habitats. In Croatia's coastal areas, there is a need for conservation of genetic resources of Dalmatian black pine (P. nigra ssp. dalmatica) and Mediterranean oaks.