AbstractSince 2008,Colombia has been experiencing an epidemic of the coffee rustHemileia vastatrix. The altitude range of the disease has expanded, and nursery and young plants that were usually not attacked by the disease are now significantly affected. To determine whether this new epidemic has been caused by a new pathogenic isolate, the molecular diversity of the pathogen causing the epidemic in different regions of the country was assessed, usingAFLPmolecular markers on isolates collected from coffee fields prior and after the year 2008. We also evaluated the aggressiveness of isolates collected from diverse coffee‐producing areas and from different coffee genotypes. Isolates collected before and during the present epidemic were quite similar both genetically and with regard to their aggressiveness. Out of a total of 349 fragments amplified from 6AFLPprimer combinations, 48 (13.2%) were polymorphic and only 18 were unique amongH. vastatrixisolates representative of pre‐2008 and post‐2008 epidemic populations. We conclude that the epidemic was caused by the excessive rainfall that has occurred inColombia since 2006 and that extended to 2011 and not by the arrival of a new isolate of the pathogen or a change in virulence of the species present in the country.