The recurrent evolutionary emergence of asexual lineages within sexual zoo- and anthropophilic dermatophyte species living in animal-frequented soil is likely to be triggered by changes in ecological niche, i.e., shifts of host animal. Subsequent adaptation to the new host species is noted. Sometimes geographic isolation or intrinsic host factors like human race may also play a role in speciation. In the present study, we elaborate concepts of speciation in dermatophytes using the Microsporum canis complex as an example. The group consists of a cluster of phylogenetically closely related anamorphs: the anthropophilic taxa Microsporum audouinii and M. ferrugineum, and the zoophilic taxon M. canis. The sexually reproducing species underlying this complex is Arthroderma otae. The study is done by an analysis of the population structure of about 200 isolates and using intergenic spacers, non-translated regions of genes as well as hypervariable microsatellite markers that are known to evolve at high mutation rates. The results suggest that sympatric speciation took place already during the period where mating ability was maintained and thus that strictly clonal fungal species emerged in Africa and led to genetically isolated clonal species elsewhere.