Little is known of the potential coevolution of flowers and bees in changing, biodiverse environments. Female solitary bees, megachilids and Centris, and their nest pollen provisions were monitored with trap nests over a 17-year period in a tropical Mexican biosphere reserve. Invasion by feral Apis (i.e. Africanized honey bees) occurred after the study began, and major droughts and hurricanes occurred throughout. Honey bee competition, and ostensibly pollination of native plants, caused changes in local pollination ecology. Shifts in floral hosts by native bees were common and driven by plant phylogenetics, whereby plants of the same families or higher taxa were substituted for those dominated by honey bees or lost as a result of natural processes.