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Banyan trees are distinguished by their extraordinary aerial roots. The Ficus genus includes species that have evolved a species-specific mutualism system with wasp pollinators. We sequenced genomes of the Chinese banyan tree, F. microcarpa , and a species lacking aerial roots, F. hispida, and one wasp genome coevolving with F. microcarpa , Eupristina verticillata. Comparative analysis of the two Ficus genomes revealed dynamic karyotype variation associated with adaptive evolution. Copy number expansion of auxin-related genes from duplications and elevated auxin production are associated with aerial root development in F. microcarpa. A male-specific AGAMOUS paralog, FhAG2 , was identified as a candidate gene for sex determination in F. hispida. Population genomic analyses of Ficus species revealed genomic signatures of morphological and physiological coadaptation with their pollinators involving terpenoid- and benzenoid-derived compounds. These three genomes offer insights into and genomic resources for investigating the geneses of aerial roots, monoecy and dioecy, and codiversification in a symbiotic system. • Genomes of two Ficus species and one wasp pollinator revealed fig-wasp coevolution • Aerial root formation is triggered by an auxin-dependent pathway promoted by light • A male-specific FhAG2 gene is a candidate gene for sex determination in F. hispida • Genes related to coadaptation contribute to codiversification between fig and wasp Comparative analyses of two Ficus genomes with and without aerial roots reveal insights into the genomic basis of aerial root formation and population genomic analyses of Ficus species alongside the genome of a coevolving wasp pollinator enhance our understanding of their species-specific mutualism. [ABSTRACT FROM AUTHOR]