Group I and group II introns are known as mobile selfish genetic elements. Their phylogenetic distribution is widespread and often sporadic because of dynamic equilibrium between evolutionary gains and losses of the elements. To investigate the evolutionary dynamics of these introns, endoparasitic fungi of the genus Cordyceps are good candidates. The reasons are as follows: 1) they contain a number of group I and group II introns in nuclear and mitochondrial ribosomal RNA genes (rDNAs), 2) these introns showed highly polymorphic insertion patterns in the single fungus genus Cordyceps, 3) the phylogenetic relationships among Cordyceps have been extensively analyzed. From our molecular phylogenetic analyses, the evolutionary dynamics of multiple selfish introns in Cordyceps fungi was inferred as follows: 1) most of the group I introns were already present at the 8 sites in small subunit (SSU) and large subunit (LSU) rDNAs of the ancestor of the genus Cordyceps; 2) the group I introns have principally been immobile and vertically transmitted throughout speciation and diversification of Cordyceps fungi, which resulted in the phylogenetic congruence between the introns at the same site and their hosts; 3) in the course of vertical transmission, the group I introns have repeatedly been lost in a number of lineages independently, which led to the present sporadic phylogenetic distribution of the introns; and 4) a few acquisitions of new introns, presumably through horizontal transmission, were identified in the evolutionary history of the genus Cordyceps, while no transpositions were detected. Losses of group I introns in nuclear SSU rDNA have occurred at least 27 times in the evolutionary course of the 28 Cordyceps members.