Recent molecular analyses indicate that many reef coral species belong to hybridizing species complexes or ‘‘syngameons.’’ Such complexes consist of numerous genetically distinct species or lineages, which periodically split and/or fuse as they extend through time. During splitting and fusion, morphologic intermediates form and species overlap. Here we focus on processes associated with lineage fusion, and the recognition of such hybridization in the fossil record. Our approach involves comparing patterns of ecologic and morphologic overlap in genetically characterized modern species with fossil representatives of the same or closely related species. We also consider the long-term consequences of past hybridization on the structure of modern-day species boundaries. Our studies involve the species complex Montastraea annularis s.l., with which we also conduct parallel studies on long-term evolutionary history, palaeoecology, and rates of origination and extinction.