A comprehensive database of pitaya would facilitate studies of pitaya and the other Cactaceae plant species. Here, we constructed pitaya genome and multiomics database (PGMD; http://www.pitayagenomic.com), a database which is a collection of the most updated and high-quality pitaya genomic assembly and contains various information including genomic variation, gene expression, miRNA profiles, metabolite and proteomic data from various tissues and fruit developmental stages of different pitaya cultivars. In PGMD, we also uploaded videos on the flower development of pitaya and planting tutorials for practical usage. Overall, these valuable data provided in the PGMD will significantly facilitate future studies on population genetics, molecular breeding and function research of pitaya.