In 2003, three Frankia strains - CcI3, Ean1pec and ACN14a - entered the genome sequencing pipeline. CcI3 and Ean1pec were sequenced at the Joint Genome Institute (JGI) in a collaboration between D. Benson at the University of Connecticut and L. Tisa at the University of New Hampshire together with Dr. M. Pilar Francino at JGI. The third was initiated independently by P. Normand at the Université Lyon in collaboration with scientists from Genoscope in France and several other groups. The first description of the genomes has been published in Genome Research.

Several Frankia genomes are now complete and available through GenBank. They represent strains from Clusters 1, 2 and 3 that infect a wide variety of plants, as well as from several related actinomycetes such as Acidothermus cellulolyticus 11B^T, Blastococcus saxobsidens DD2^T, Geodermatophilus obscurus G-20^T, Kineococcus radiotolerans ATCC BAA-149^T, Modestobacter marinus BC501, Nakamurella multipartita DSM 44233^T, and Sporichthya polymorpha DSM 43042^T (Nouioui et al., 2019).