MolliGen is a database dedicated to the comparative genomics and the genome engineering of bacteria belonging to the class Mollicutes. MolliGen provides tools for exploration and comparison of 408 genomes belonging to 163 species. Most genomes included in MolliGen are public genomes retrieved from databases such as EMBL or GenBank. A private access to store, analyze and compare your favorite unpublished genome in MolliGen is available upon request. As cutting-edge synthetic biology methods have been recently developed for a growing number of mollicute species, a specific module is now available in MolliGen to help designing genome engineering experiments.