Licorice (Glycyrrhiza L.), a medicinally and economically significant genus in the Fabaceae, is known for synthesizing glycyrrhizin. Here, we present a newly assembled genome of Glycyrrhiza uralensis, a key species distributed across Central and East Asia. Using Oxford Nanopore, Hi-C, and Illumina sequencing, we assembled a 415 Mbp genome with an N50 of 47 Mbp. While the genome structure was similar to previously reported assemblies, structural variations were observed across all eight chromosomes. Re-sequencing data from 29 individuals, including G. uralensis, G. glabra, and their hybrids, revealed significant genetic diversity, population structure, and hybridization events. Phylogenomic analyses using nuclear and plastid genomes demonstrated phylogenetic incongruence, supporting hybridization between G. uralensis and G. glabra. Our species network and gene flow test identified hybrid groups (Ggu1, Ggu2, and Gug) acting as genetic bridges between the species. Demographic history inferred via PSMC showed Glycyrrhiza species thrived during the Middle Pleistocene, with population size fluctuations in G. uralensis and hybrids. Current low heterozygosity and high genetic differentiation suggest long-term geographic and ecological isolation, reducing gene flow. Our findings advance the understanding of evolutionary history in Glycyrrhiza species and help conservation and molecular breeding of these species.