CitGVD is the first comprehensive database dedicated to citrus genomic variations, featuring over 1.49 billion high-quality SNPs and INDELs from 346 citrus accessions, along with 84 phenotypes. It integrates two reference genomes (Citrus clementina and Citrus grandis) and provides tools for browsing, searching, GWAS, evolutionary analysis, primer design, and data download. Built on MySQL and J2EE, CitGVD offers free, user-friendly access to support molecular breeding and genetic research in citrus. Future updates will include more structural variants, metabolome data, and marker-assisted selection tools.