Orchids have evolved special morphological structures and survival strategies, including highly specialized plant-pollinator relationships, an epiphytic lifestyle and orchid mycorrhizae, which set them apart from other vascular plants. Here, Chao et al. (pp e1- e13) describe Orchidstra 2.0 (http://orchidstra2.abrc.sinica.edu.tw), which has been built with a new database system to accommodate 510,947 protein-coding gene annotations and gene expression data across various tissues, covering 18 orchid species belonging to 12 genera in 5 subfamilies of the Orchidaceae. One of the unique new features in Orchidstra 2.0 is the pre-computed orthologous genes across orchid species and model organisms, which is an important starting point for transferring the acquired knowledge between species, and is therefore very useful for genome annotation and comparative genomics. Orchidistra 2.0 forms part of a collection of 10 database papers featured in this year’s 2017 online Database Issue.