As one of the main origin centers of nut trees, Iran is the fourth leading nut crops producer in the world (6% of total nut production). Due to the high genetic diversity, development of new varieties and rootstocks with desirable characteristics have been highly considered by fruit breeders in Iran. In this regard, molecular breeders concentrate on filling the gaps in the conventional breeding with the aim of accelerating breeding programs. Recent advancements in molecular breeding such as next-generation sequencing (NGS) techniques, high-throughput genotyping platforms and genomics-based approaches including genome wide association studies (GWAS), and genomic selection (GS) have opened up new avenues to enhance the efficiency of nut trees breeding. Over the past decades, Iranian nut crops breeders have successfully used advanced molecular and genomic tools such as molecular markers, genetic transformations and high-throughput genotyping to explore the genetic basis of the desired traits and eventually to develop new varieties and rootstocks. Due to a broad international cooperation, a clear perspective is envisaged for the nut breeding programs in Iran, especially based on new biotechnology techniques. The propagation of nut trees in Iran have also been dramatically improved. Different types of grafting and tissue culture (micropropagation or somatic embryogenesis) techniques for propagation of nut crops have been studied intensively in the last 30 years in Iran and the successful techniques have been commercialized. Several certified nurseries are producing grafted and micropropagation plants of walnut, pistachio and other nut crops commercially. A part of the grafted and micropropagaited plants of nut crops in Iran is being exported to the other countries. Establishing modern orchards of nut crops using new cultivars and rootsocks is presently being advised by professional consultants.