The phylogeny of 13 species of Myricaceae, the most ancient actinorhizal family involved in a nitrogen-fixing symbiosis with the actinomycete Frankia, was established by the analysis of their rbcL gene and 18S-26S ITS. The phylogenetic position of those species was then compared to their specificity of association with Frankia in their natural habitat and to their nodulation potential determined on greenhouse-grown seedlings. The results showed that Genus Myrica, including M. gale and M. hartwegii, and Genus Comptonia, including C. peregrina, belong to a phylogenetic cluster distinct from the other Myrica species transferred in a new genus, Morella. This grouping parallels the natural specificity of each cluster with Comptonia–Myrica and Morella being nodulated by two phylogenetically divergent clusters of Frankia strains, the Alnus and Elaeagnaceae-infective strains clusters, respectively. Under laboratory conditions, Comptonia and Morella had a nodulation potential larger than under natural conditions. From this study it appears that the Myricaceae are split into two different specificity groups. It can be hypothesized that the early divergence of the genera led to the selection of genetically diverse Frankia strains which is contradictory to the earlier proposal that evolution has proceeded toward narrower promiscuity within the family.