Partners in obligate mutualisms often contribute complementary elements to joint pathways for synthesizing or degrading metabolites. Their committed cooperation can make new niches accessible, with evolutionary diversification and speciation as possible consequences. However, when individual partners vary in metabolic performance, division of labour may not always be optimized and co-evolutionary trajectories become less predictable. The higher fungus-growing (attine) ants consist of the leafcutter ants (Acromyrmex and Atta), which rear a single fungal species throughout their Latin American range, and a paraphyletic assembly of Trachymyrmex and Sericomyrmex species that cultivate more genetically diverse fungal symbionts. Leaf-decomposition productivity of colonies depends on the combined efforts of ant foragers collecting and macerating plant material and fungal enzymes excreted directly or indirectly via ant fecal fluid. We determined the interaction specificity between ant species and fungal strains across sympatric populations of six Trachymyrmex and Sericomyrmex species in Panama, and established that these ants jointly reared eight fungal haplotype groups that differed significantly in garden enzyme activity independent of ant species association. This illustrates that the mosaic of coevolutionary interactions in Trachymyrmex and Sericomyrmex fungus-growers may be fundamentally different from the interactions in Acromyrmex and, particularly, Atta leaf-cutting ants. The former appear to be analogous to a diverse array of subsistence farming practices at the mercy of local conditions, whereas the latter resemble large-scale, low-diversity “industrial” farming.