Objectives <p>The draft genome assembly was generated within the framework of a greater study aiming to investigate the differences in genomic features characterizing freshwater gastropod species differing in their threat status according to the IUCN assessments. </p> Data description <p>Mollusca is among the most species-rich animal groups, yet their genomes are underrepresented in genomic databases. Major drawbacks for this are the complexity of Mollusca genomes as well as the fact that due to the presence of mucopolysaccharides in their tissues, they tend to provide low quality DNA extracts. Therefore, the generation of high-quality Molluscan genome assemblies is a challenging issue. The <i>A. crista</i> draft genome of the present study will serve as an addition to the planorbid genomes assembled today representing three different genera (<i>Anisus</i>, <i>Biomphalaria</i>, <i>Bulinus</i>). Therefore, it will serve as an additional genomic asset in the effort to elucidate the ecology, evolution and taxonomy of the highly diverse taxon of Mollusca. </p>