The Juglans plants are economically important as they provide nuts, wood and garden trees. They also play an important ecological role by supplying food for wild insects and animals. The decoding of genome sequences has fundamental values for understanding the evolution of Juglans plants and molecules, and is also a prerequisite for molecular breeding. During the last three years, the rapid development of sequencing technology has made walnut research into the genome era. Here, we reviewed the progress of genome sequencing of six Juglans species, the resequencing of four Juglans populations as well as the genome sequencing of the closely related species Pterocarya stenoptera. The analysis of the Juglans regia genome uncovers a whole genome duplication (WGD) event. Based on the molecular dating of the divergence time of six Juglans species, we proposed this WGD event was associated with Cretaceous-Palaeogene (K-Pg) boundary occurred ∼65 million years ago. Genomic sequences also provide clear details for understanding the evolution and development of GGT and PPO genes involved in fruit development. The decoding of these genomes has made it easier for us to understand and enhance the use of walnuts. We expect that the functional genomics research of walnut will also develop rapidly in the near future.