The Ensembl project was started in 1999, some years before the draft human genome was completed. Even at that early stage it was clear that manual annotation of 3 billion base pairs of sequence would not be able to offer researchers timely access to the latest data. The goal of Ensembl was therefore to automatically annotate the genome, integrate this annotation with other available biological data and make all this publicly available via the web. Since the [website's launch in July 2000](http://web.archive.org/web/20000815203739/http://www.ensembl.org/), many more genomes have been added to Ensembl and the range of available data has also expanded to include comparative genomics, variation and regulatory data.
In 2009, the Ensembl Genomes project was launched with specific web portals for plant, fungal, invertebrate metazoan, bacterial and protist genomes. These aim to provide taxonomic reference points giving evolutionary context in which genes can be understood, as well as coverage of all major non-vertebrate experimental organisms, species of agricultural importance, pathogens and vectors. By 2020, Ensembl supported over 50,000 genomes across the Ensembl and Ensembl Genomes websites including [Rapid Release](https://rapid.ensembl.org/), which gives fast access to freshly annotated genomes, and [COVID-19](https://covid-19.ensembl.org/), providing access to the SARS-CoV-2 genome.
