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species are life-threatening human fungal pathogens that cause cryptococcal meningoencephalitis in both immunocompromised and healthy hosts. The natural environmental niches of include pigeon () guano, soil, and a variety of tree species such as , and spp. Genetic and genomic studies of extensive sample collections have provided insights into the population distribution and composition of different species in geographic regions around the world. However, few such studies examined in Turkey. We sampled 388 (olive) and 132 . trees from seven locations in coastal and inland areas of the Aegean region of Anatolian Turkey in September 2016 to investigate the distribution and genetic diversity present in the natural population. We isolated 84 strains (83 α and 1 ) and 3 strains (all α) from 87 (22.4% of surveyed) . trees; a total of 32 . strains were isolated from 32 (24.2%) of the . trees, all of which were α. A statistically significant difference was observed in the frequency of . isolation between coastal and inland areas ( 0.05). Interestingly, the . isolate was fertile in laboratory crosses with VNI and VNB α tester strains and produced robust hyphae, basidia, and basidiospores, thus suggesting potential sexual reproduction in the natural population. Sequencing analyses of the gene identified at least five different genotypes among the isolates. Population genetics and genomic analyses revealed that most of the isolates in Turkey belong to the VNBII lineage of . , which is predominantly found in southern Africa; these isolates are part of a distinct minor clade within VNBII that includes several isolates from Zambia and Brazil. Our study provides insights into the geographic distribution of different . lineages in the Mediterranean region and highlights the need for wider geographic sampling to gain a better understanding of the natural habitats, migration, epidemiology, and evolution of this important human fungal pathogen.