AIM The aim of this work was to identify the main changes in the flora and vegetation of the Iberian Peninsula over the Cenozoic Era, to record the disappearance of taxa associated with these changes and to determine the influence of climate and human activity on these events. Location The Iberian Peninsula and Balearic Islands. METHODS A critical review was made of the palaeobotanical literature with the aims of detecting patterns of floristic change and extracting information on the disappearance of different taxa over the Cenozoic. These data are viewed alongside the most recent data for the climate of this period. A critical analysis is made of the role of Palaeotropical and Arctotertiary taxa in the forest communities of the Iberian Peninsula throughout the Cenozoic. RESULTS Although the Eocene–Oligocene transition was a time when many taxa disappeared, the most outstanding events occurred between the end of the Oligocene and throughout the Miocene. Substantial floristic changes took place over this period, including the disappearance of 177 Palaeotropical taxa. This was probably related to acute cooling and aridification; no evidence exists that the Messinian Salinity Crisis had any important effect in the Iberian Peninsula. The last great disappearance of Palaeotropical taxa (36 in total) ended in the Middle–Late Piacenzian; Arctotertiary taxa were most affected during the Pleistocene. The Lower–Middle Pleistocene transition, best represented by marine isotopic stages (MIS) 36–34 and 20–18 and characterized by a change in glacial cyclicity, was the time of the last notable disappearance of taxa. MAIN CONCLUSIONS This work provides the first chronogram of extinctions for the Iberian flora, and records the disappearance of 277 taxa during the Cenozoic. A clear relationship was detected between the main climatic events and the latest appearances of the different taxa