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SUMMARY: Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological and ecological diversity. Here, we report a high‐quality chromosome‐level genome assembly for Euscaphis japonica, an early‐diverging species within malvids. Genome‐based phylogenetic analysis suggests that the unstable phylogenetic position of E. japonica may result from incomplete lineage sorting and hybridization event during the diversification of the ancestral population of malvids. Euscaphis japonica experienced two polyploidization events: the ancient whole genome triplication event shared with most eudicots (commonly known as the γ event) and a more recent whole genome duplication event, unique to E. japonica. By resequencing 101 samples from 11 populations, we speculate that the temperature has led to the differentiation of the evergreen and deciduous of E. japonica and the completely different population histories of these two groups. In total, 1012 candidate positively selected genes in the evergreen were detected, some of which are involved in flower and fruit development. We found that reddening and dehiscence of the E. japonica pericarp and long fruit‐hanging time promoted the reproduction of E. japonica populations, and revealed the expression patterns of genes related to fruit reddening, dehiscence and abscission. The key genes involved in pentacyclic triterpene synthesis in E. japonica were identified, and different expression patterns of these genes may contribute to pentacyclic triterpene diversification. Our work sheds light on the evolution of E. japonica and malvids, particularly on the diversification of E. japonica and the genetic basis for their fruit dehiscence and abscission. Significance Statement: Malvids is one of the largest clades of rosids and include 58 families, and its phylogenetic position is still contested. Euscaphis japonica, an early‐diverging species within malvids, is mainly distributed in Southeast Asia with deciduous or evergreen and two types: deciduous and evergreen. We assembled a high‐quality chromosome level genome of E. japonica, and found that E. japonica experienced a unique whole genome duplication event approximately 53 Mya. Genome‐based phylogenetic analysis suggests that the unstable phylogenetic position of E. japonica may result from incomplete lineage sorting and hybridization event during the diversification of the ancestral population of malvids. By resequencing 101 samples from 11 populations, we speculate that the temperature has led to the differentiation of the evergreen and deciduous of E. japonica and the completely different population histories of these two groups. Candidate positively selected genes related to the flower and fruit development in the evergreen were detected. We found that reddening and dehiscence of the E. japonica pericarp and long fruit‐hanging time promoted the reproduction of E. japonica populations, and revealed the expression patterns of genes related to fruit reddening, dehiscence, and abscission. The key genes involved in pentacyclic triterpene synthesis in E. japonica were identified, and different expression patterns of these genes may contribute to pentacyclic triterpene diversification. In summary, the present study has important scientific significance because it describes the phylogeny of the malvids, how the ancestor E. japonica differentiates into the evergreen and deciduous, and the evolutionary significance of the fruit. [ABSTRACT FROM AUTHOR]