Partner fidelity through vertical symbiont transmission is thought to be the primary mechanism stabilizing cooperation in the mutualism between fungus-farming (attine) ants and their cultivated fungal symbionts. An alternate or additional mechanism could be adaptive partner or symbiont choice mediating horizontal cultivar transmission or de novo domestication of free-living fungi. Using microsatellite-genotyping for the attine ant Mycocepurus smithii and ITS rDNA-sequencing for fungal cultivars, we provide the first detailed population-genetic analysis of local ant-fungus associations to test for the relative importance of vertical versus horizontal transmission in a single attine species. M. smithii is the only known asexual attine ant, and it is furthermore exceptional because it cultivates a far greater cultivar diversity than any other attine ant. Cultivar switching could permit the ants to re-acquire cultivars after garden loss, to purge inferior cultivars that are locally mal-adapted or that accumulated deleterious mutations under long-term asexuality. Compared to other attine ants, symbiont choice and local adaptation of ant-fungus combinations may play a more important role than partner fidelity feedback in the co-evolutionary process of M. smithii and its fungal symbionts.