Evolutionary processes in ant-plant mutualisms are mediated by intrinsic features of the association and by change through time in abiotic components of the system (e.g. geography and climate). Incorporating both biotic and abiotic components and the phylogenies of the taxa involved is central to understanding their respective roles in mutualism evolution. We used a comparative phylogeographic approach to assess the effects of the Andean uplift on the mutualism between Azteca ants and an ant plant, Tococa guianensis , and to ask whether plant and ant diversification were promoted by geography or by the association. We used a combination of nuclear and organellar sequence data to resolve relationships between populations of ants and plants at sites spanning the northern Andes Cordillera in Colombia. To test for phylogenetic and chronological congruence between taxa and major uplift events, we used fossil calibrations and estimated the timing of diversification. We found phylogeographic structure in both Azteca and T. guianensis that coincides spatially and temporally with peaks of activity during the Andean uplift. However, lineage divergence occurs earlier in Azteca than in T. guianensis . We suggest that the Andean uplift had a greater impact on lineage diversification than did the mutualism. • The evolution of Azteca-Tococa guianensis mutualism is consistent with ecological fitting and not with co-diversification. • The effect of the Andean uplift differs between ant and plant lineages; Azteca diversified earlier than Tococa guianensis . • Geographic structure of Azteca and Tococa populations is trans-Andean and consistent with vicariance. • The Northern Andes cordillera is porous barrier to gene flow between populations located near low heights (<1600 masl).